diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..cb3c3c0 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,3 @@ +^.*\.Rproj$ +^\.Rproj\.user$ +^LICENSE diff --git a/DESCRIPTION b/DESCRIPTION index e758e4e..26cfdd9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,18 +1,42 @@ Package: RepliSeq Type: Package -Title: Repliseq -Version: 0.0.0.9000 -Author: Sami EL HILALI +Title: Process Repli-Seq data to analyze the DNA replication timing +Version: 0.1.1 +Authors@R: c(person(given="Sami", + family ="El Hilali", + email = "elhilali.sami@gmail.com", + role = c("aut", "cre"), + comment = c(ORCID = "0000-0003-4417-8399")), + person(given="Chun-Long", + family="Chen", + role = "aut", + comment = c(ORCID = "0000-0002-4795-0295"), + person(given="Stefano", + family="Gnan", + role = "ctb", + comment = c(ORCID = "0000-0003-3314-4302")) + ) Maintainer: Sami EL HILALI -Description: This Package contains a set of functions for the analysis of Repli-Seq data to study DNA replication timing program. These functions handles repliseq assays as data frames from count matrices (bedgraph format !!) and performs such things as rescaling, data normalization, replication timing calculation (S50), URI calculation. -License: GPL-3 +Depends: R (>= 4.1.0) +Imports: + dplyr, + magrittr, + RColorBrewer, + ggplot2, + corrplot, + reshape2 +Description: This Package contains a set of functions for the analysis of Repli-Seq data to + study DNA replication timing program. These functions handles repliseq assays as data frames + from count matrices (Bedgraph format) and performs rescaling, data normalization, + replication timing calculation (S50), URI calculation. Encoding: UTF-8 LazyData: true -RoxygenNote: 7.1.0 +License: GPL-3 +URL: https://github.com/SamiLhll/RepliSeq +BugReports: https://github.com/SamiLhll/RepliSeq/issues +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.2.1 Suggests: knitr, rmarkdown VignetteBuilder: knitr -Imports: - dplyr (>= 0.8.3), - magrittr (>= 1.5) diff --git a/NAMESPACE b/NAMESPACE index a13dc2c..6b0e183 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -7,13 +7,25 @@ export(doubleXchr) export(normalizeRS) export(readRS) export(removeNoise) +export(repliseqCorrPlot) +export(repliseqDensityPlot) export(rescaleRS) export(smoothRS) export(weight_phases) export(writeBedgraph) export(writeBigwig) +import(ggplot2) import(magrittr) +importFrom(RColorBrewer,brewer.pal) +importFrom(corrplot,corrplot) +importFrom(corrplot,corrplot.mixed) importFrom(dplyr,funs) importFrom(dplyr,mutate_each) importFrom(dplyr,rename) importFrom(dplyr,select) +importFrom(reshape2,melt) +importFrom(stats,cor) +importFrom(stats,cor.test) +importFrom(stats,density) +importFrom(utils,read.table) +importFrom(utils,write.table) diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..f7d9f0d --- /dev/null +++ b/NEWS.md @@ -0,0 +1,17 @@ +# RepliSeq 0.1.1 + +### New features : + +* Added the function repliseqCorrPlot() to draw correlograms of several Repli-Seq assays. + +### Enhancements : + +* Added a `NEWS.md` file to track changes to the package. + +* Improved the documentation and vignette + +* repliseqDensityPlot now allows to draw counts through the argument stat, and it now has arguments to display the labels. + +### Bug fixes : + +* Fixed a bug in rescaleRS() diff --git a/R/calculateNoiseRatios.R b/R/calculateNoiseRatios.R index 971b84e..4c3401e 100644 --- a/R/calculateNoiseRatios.R +++ b/R/calculateNoiseRatios.R @@ -3,13 +3,16 @@ #' #' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx #' @param rs_control a Repli-seq control assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S0 -#' +#' @param noise_method either "max_density"(default) or "min_downslope" #' @return an array with the ratios in the order of rs_assay fractions +#' +#' @importFrom stats density +#' #' @export #' -calculateNoiseRatios <- function(rs_assay, rs_control) { +calculateNoiseRatios <- function(rs_assay, rs_control, noise_method = "max_density") { # select control and fractions : temp_fractions <- rs_assay[,!(names(rs_assay) %in% c("chr","start","stop"))] temp_control <- rs_control[,!(names(rs_control) %in% c("chr","start","stop"))] @@ -17,9 +20,15 @@ calculateNoiseRatios <- function(rs_assay, rs_control) { to_return <- NULL for (fraction in names(temp_fractions)) { temp_fraction_vs_control <- round(rs_assay[,fraction] / temp_control, digits = 3) - temp_density <- density(temp_fraction_vs_control,na.rm = TRUE) - temp_max <- which.max(temp_density$y) - temp_ratio <- round(temp_density$x[temp_max],digits = 3) + temp_density <- stats::density(temp_fraction_vs_control,na.rm = TRUE) + if (noise_method == "min_downslope") { + temp_downslopes <- which(diff(temp_density$y) < 0) + temp_ratio <- temp_density$x[min(temp_downslopes)] + } + else if (noise_method == "max_density") { + temp_max <- which.max(temp_density$y) + temp_ratio <- round(temp_density$x[temp_max],digits = 3) + } to_return <- c(to_return,temp_ratio) } return(to_return) diff --git a/R/readRS.R b/R/readRS.R index 700c9c0..1fcf686 100644 --- a/R/readRS.R +++ b/R/readRS.R @@ -1,31 +1,53 @@ -#' @title Read Repli-seq assay data (bedgraph format). -#' @description Bedgraphs with a one line header and with similar organization (same length and sorted) +#' @title Read Repli-Seq assay data (Bedgraph format). +#' @description Read and integrate all Repli-Seq fractions in a single dataframe. +#' Fractions must be formatted as Bedgraph with a one line header and with similar resolutions. #' -#' @param paths_data list of paths to repliseq fractions files -#' @param fractions list of fractions names +#' @param paths_data Array. List of paths to Repli-Seq fractions files +#' @param fraction_names Array. List of fractions names (default = S1, ..., Sn) #' #' @return a dataframe composed of genomic coordinates plus all the specified fractions as for example : chr,start,stop,S1,S2,S3,S4,S5,S6 #' @import magrittr #' @importFrom dplyr select #' @importFrom dplyr rename +#' @importFrom utils read.table +#' +#' @examples +#' # basic usage of read_RS : +#' +#' S1_path <- system.file("extdata", "NT_chr22-s1.bdg", package="RepliSeq") +#' S2_path <- system.file("extdata", "NT_chr22-s2.bdg", package="RepliSeq") +#' +#' my_rs_assay <- readRS(paths_data = c(S1_path , S2_path), +#' fraction_names = c("S1","S2")) +#' #' @export -readRS <- function(paths_data,fractions) { +readRS <- function(paths_data = NULL, + fraction_names = NULL) { + + V1 <- V2 <- V3 <- NULL + + ### Create default faction_names + if (is.null(fraction_names)) { + amount_of_fractions <- length(paths_data) + fractions_names <- paste0("S",c(1:amount_of_fractions)) + } #### Control that path data and fractions are the same length - if (length(paths_data) != length(fractions)) { + if (length(paths_data) != length(fraction_names)) { stop("arguments paths_data and fractions must have the same sizes") } ### read genomic coordinates from first fraction : - rs_temp <- read.table(paths_data[1] , header = FALSE , skip=1 , sep="") %>% + rs_temp <- utils::read.table(paths_data[1] , header = FALSE , skip=1 , sep="") %>% select(V1,V2,V3) %>% rename(chr = V1, start = V2, stop = V3) + ### read other fractions and create the corresponding columns in rs_temp for (i in c(1:length(paths_data))) { - temp_fraction <- fractions[i] + temp_fraction <- fraction_names[i] temp_path <- paths_data[i] - temp_fraction_df <- read.table(temp_path,header=FALSE,skip=1,sep="") + temp_fraction_df <- utils::read.table(temp_path,header=FALSE,skip=1,sep="") rs_temp[temp_fraction] <- temp_fraction_df$V4 } diff --git a/R/repliseqCorrPlot.R b/R/repliseqCorrPlot.R new file mode 100644 index 0000000..2398de2 --- /dev/null +++ b/R/repliseqCorrPlot.R @@ -0,0 +1,63 @@ +#' @title Calculate and plot correlation plots. +#' @description Calculate and draw a correlation plot from Repli-seq assay (data.frame) see http://www.sthda.com/french/wiki/visualiser-une-matrice-de-correlation-par-un-correlogramme +#' +#' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx +#' @param corr_method character in either "pearson","spearman" or "kendall" to use as a parameter for cor.test function +#' @param ordering a character in either "original","AOE", "FPC", "hclust", "alphabet" to reorder the compared variables (to fill the corrplot() order parameter ) +#' @param plottype from corrplot type argument. either "upper", "lower" or "mixed". default = "mixed". +#' +#' @return a mixed correlation plot +#' @importFrom RColorBrewer brewer.pal +#' @importFrom corrplot corrplot.mixed corrplot +#' @importFrom stats cor.test cor +#' +#' @export +#' + + +repliseqCorrPlot <- function(rs_assay, + corr_method = "pearson", + ordering = "original", + plottype="mixed") { + + temp_rs_assay <- rs_assay[,!(names(rs_assay) %in% c("chr","start","stop"))] + # ressource : http://www.sthda.com/french/wiki/visualiser-une-matrice-de-correlation-par-un-correlogramme + # Calculate correlation matrix + temp.cor <- stats::cor(temp_rs_assay,method = corr_method) + # Calculate p-values associated with each correlation + p.mat <- cor.mtest(temp.cor) + # plot the correlation matrix + if (plottype == "mixed") { + corrplot.mixed(temp.cor,is.corr = FALSE, + order=ordering, tl.col= "black",addrect = 2, + upper.col = brewer.pal(n = 10, name = "PuOr"), + lower.col= brewer.pal(n = 10, name = "PuOr"), + tl.cex=0.8,number.cex = 0.8,cl.cex = 0.8) + } + else { + corrplot(temp.cor,is.corr = FALSE, type = plottype, + order=ordering, tl.col="black",addrect = 2, + upper.col = brewer.pal(n = 10, name = "PuOr"), + lower.col= brewer.pal(n = 10, name = "PuOr"), + tl.cex=0.8,number.cex = 0.8,cl.cex = 0.8) + } + +} + +########### + +# Calculation of the p-values associated with a correlation matrix +cor.mtest <- function(mat, ...) { + mat <- as.matrix(mat) + n <- ncol(mat) + p.mat<- matrix(NA, n, n) + diag(p.mat) <- 0 + for (i in 1:(n - 1)) { + for (j in (i + 1):n) { + tmp <- stats::cor.test(mat[, i], mat[, j], ...) + p.mat[i, j] <- p.mat[j, i] <- tmp$p.value + } + } + colnames(p.mat) <- rownames(p.mat) <- colnames(mat) + p.mat +} \ No newline at end of file diff --git a/R/repliseqDensityPlot.R b/R/repliseqDensityPlot.R new file mode 100644 index 0000000..12ea985 --- /dev/null +++ b/R/repliseqDensityPlot.R @@ -0,0 +1,50 @@ +#' @title Calculate and plot density plots. +#' @description Calculate and draw a density plot from Repli-seq assay (data.frame) +#' +#' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx +#' @param grided boolean (default = F) if True then each fraction s displayed on a different panel, otherwise all the fractions are colored in a single panel +#' @param stat "counts" (default) or "density" to use in the stat argument +#' @param ncols (default = 3) amount of columns when grided == T (see ggplot2 facet_wrap ncol parameter) +#' @param rs_resolution resolution of the rs_assay to display in the labels in the plots. Default equals "50kb" +#' +#' @return a ggplot object displaying density for the provided repliseq assay +#' @import ggplot2 +#' @importFrom reshape2 melt +#' @export +#' + + +repliseqDensityPlot <- function (rs_assay, + stat = "counts", + grided = F, + ncols = 3, + rs_resolution = "50kb") { + + value <- variable <- NULL + # extract and melt the fractions : + temp_fractions <- rs_assay[,!(names(rs_assay) %in% c("chr","start","stop"))] + temp_fractions_melted <- melt(temp_fractions) + + + label_x <- paste0("Counts of reads / ",rs_resolution, "windows") + label_y <- paste0(stat," of windows") + + # grided plot : + if (grided) { + p <- ggplot(temp_fractions_melted,aes(x = value)) + + geom_line(stat=stat) + + facet_wrap(~ variable,ncol=ncols) + + theme_bw(20) + + labs(x = label_x, y = label_y) + } + + # not grided plot : + else { + p <- ggplot(temp_fractions_melted,aes(x = value,color=variable)) + + geom_line(stat=stat) + + theme_bw(20) + + labs(x = label_x, y = label_y ,color="sample") + } + + return(p) +} \ No newline at end of file diff --git a/R/rescaleRS.R b/R/rescaleRS.R index 1934c87..19239eb 100644 --- a/R/rescaleRS.R +++ b/R/rescaleRS.R @@ -13,7 +13,10 @@ #' -rescaleRS <- function(rs_assay,scale_factor) { +rescaleRS <- function(rs_assay, + scale_factor) { + + chr <- NULL # calculate_inital scale : initial_scale <- (rs_assay$stop - rs_assay$start)[1] # get names @@ -21,7 +24,7 @@ rescaleRS <- function(rs_assay,scale_factor) { rs_fractions <- rs_names[rs_names != "chr" & rs_names != "start" & rs_names != "stop"] # initialize to_return variable to_return <- NULL - rs_chroms <- levels(unique(rs_assay$chr)) + rs_chroms <- unique(rs_assay$chr) # iterate on chroms : for (i in rs_chroms) { # select data : diff --git a/R/smoothRS.R b/R/smoothRS.R index d60975b..761f2ed 100644 --- a/R/smoothRS.R +++ b/R/smoothRS.R @@ -13,7 +13,11 @@ #' -smoothRS <- function(rs_assay,smooth_factor) { +smoothRS <- function(rs_assay, + smooth_factor) { + + chr <- NULL + # calculate_inital scale : initial_scale <- (rs_assay$stop - rs_assay$start)[1] # get names diff --git a/R/writeBedgraph.R b/R/writeBedgraph.R index 2705595..4591d12 100644 --- a/R/writeBedgraph.R +++ b/R/writeBedgraph.R @@ -6,6 +6,8 @@ #' @param sample_name a string for the file names #' @param system_separator default is "/" as dedicated for linux file system #' +#' @importFrom utils write.table +#' #' @return NULL #' @export #' @@ -21,6 +23,6 @@ writeBedgraph <- function(rs_assay,path_file,sample_name,system_separator = "/") to_write <- temp_coords to_write[i] <- temp_fraction file_name <- paste0(path_file,system_separator,sample_name,"-",i,".bdg") - write.table(to_write,file = file_name,quote = FALSE, col.names = header,row.names = FALSE) + utils::write.table(to_write,file = file_name,quote = FALSE, col.names = header,row.names = FALSE) } } \ No newline at end of file diff --git a/R/writeBigWig.R b/R/writeBigWig.R index c81ebfa..5a897d3 100644 --- a/R/writeBigWig.R +++ b/R/writeBigWig.R @@ -10,6 +10,8 @@ #' @param wiggle_span a numeric value for wiggle header #' @param system_separator default is "/" as dedicated for linux file system #' +#' @importFrom utils write.table +#' #' @return NULL #' @export #' @@ -29,7 +31,7 @@ writeBigwig <- function(rs_assay,path_file,sample_name,chromsizes,wiggle_start,w } # write wiggle ; convert to BigWig and rm wiggle : file_name <- paste0(path_file,system_separator,sample_name,"-",i,".wig") - write.table(to_write,file = file_name,quote = FALSE, col.names = temp_header,row.names = FALSE) + utils::write.table(to_write,file = file_name,quote = FALSE, col.names = temp_header,row.names = FALSE) system(paste0("wigToBigWig -clip ",file_name," ",chromsizes," ",file_name,".bw")) system(paste0("rm ",file_name)) } diff --git a/README.md b/README.md index 13402ee..0e5ef90 100644 --- a/README.md +++ b/README.md @@ -1,69 +1,44 @@ -# RepliSeq -[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) +# RepliSeq -Analysis of Repli-Seq data to study DNA replication timing program in R. +This is an R package which aims at processing Repli-seq data. It takes raw counts (Bedgraph file format) as input and makes it then quick and easy to further analyze the DNA replication timing with a set of functions to manipulate and vizualize the data. +RepliSeq functions include **loading** multi-fraction Repli-seq assay data as count matrices (from 2 to N fractions depending on the experimental design) but also **rescaling** profiles to any resolution and calculting the **Replication timing** as the S50 (moment in the S-phase where a loci reaches 50% of its total replication on a scale from 0, early, to 1, late) + + [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) + -## Description: - -An R package that features a set of functions to conduct Repli-seq data analysis. - -We propose this package to analyze Repli-seq data within data.frames, which lets you easily complete your analysis with dplyr, calculate intersections with tidygenomics and plot your results with ggplot vizualizations. - -RepliSeq functions include **loading** multi-fractions (from 2 to N fractions defined by your experiment dessign and your hardware capabilities) Repli-seq assay data as count matrices; **rescaling** profiles; **smoothing** profiles; calculting metrics such as **Replication timing** (calculated as the S50, on a scale from 0, early, to 1, late, which is the moment in S phase when a sequence has been replicated in 50% of cells replication timing) and **URI** (Under replication index got from two repliseq assays comparison). +----------------------------------------------------------------------- ## Installation: You can install this package by entering the following within R: ```{r} - -devtools::install_github("CL-CHEN-Lab/RepliSeq") +# get the development version from GitHub using devtools : +# install.packages("devtools") +devtools::install_github("SamiLhll/RepliSeq",build_vignettes = TRUE) +# building the vignette makes the installation a bit longer but its mandatory so ou can access it by doing : +vignette("RepliSeq") ``` ## Requirements: -This package depends on: - -* R version >= 3.4.4 (2018-03-15) - -As mentionned in the DESCRIPTION, this packages imports: - -* dplyr (>= 0.8.3) -* magrittr (>= 1.5) - -In addition, the function **writeBigWig()** requires UCSC's **wigToBigWig** application to be installed on the computer. It can be found at [encodeproject](https://www.encodeproject.org/software/wigtobigwig/) - - - -## Authors: - -[Sami EL HILALI](mailto:elhilali.sami@gmail.com) and [Chunlong CHEN](mailto:chunlong.chen@curie.fr) (Institut Curie) - -Don't hesitate to contact the authors or open an issue for a question or if you wish to see new features to be added to this package. - - - -## References: - -Brison O., El-Hilali S., Azar, D., Koundrioukoff1 S., Schmidt M., Naehse-Kumpf V., Jaszczyszyn Y., Lachages A.M., Dutrillaux B., Thermes C., Debatisse M. and Chen C.L. (2019) [Transcription-Mediated Organization of the Replication Initiation Program Across Large Genes Sets Up Common Fragile Sites Genome-Wide.](https://doi.org/10.1038/s41467-019-13674-5) ***Nat. Commun.*** 10, 5693 - -Chen C.L., Rappailles A., Duquenne L., Huvet M., Guilbaud G., Farinelli L, Audit B, d'Aubenton-Carafa Y., Arneodo A., Hyrien O. and Thermes C. (2010) [Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes](https://genome.cshlp.org/content/20/4/447.long). ***Genome. Res.*** 20, 447-457. - +The function **writeBigWig()** requires UCSC's **wigToBigWig** application to be installed on the computer. +It can be found at [encodeproject](https://www.encodeproject.org/software/wigtobigwig/) -## Usage examples: +## Usage : -We propose an overview of some function usage. For extended documentation, please refer to the Vignette *how-to-use*. +Check out the vignette for extended documentation. -#### readRS(path_data,fractions): +#### Loading repliseq data : -This function reads Repli-seq assays from multiple files (one file for one fraction) and outputs a dataframe from it. -It requires bedgraph inputs [(see bedgraph spec)](http://genome.ucsc.edu/goldenPath/help/bedgraph.html) with a one line header but **no other comments** such as: +The function *readRS(path_data,fractions)* reads Repli-seq assays from multiple files (one file per fraction) and returns a dataframe. +It requires bedgraph inputs [(see bedgraph specifications)](http://genome.ucsc.edu/goldenPath/help/bedgraph.html) with a one line header but no other comments such as: -track type=bedGraph name=NT_chr22-s1 description=50kbprofile +track type=bedGraph name=NT_chr22-s1 description=50kb chr22 0 50000 0 chr22 50000 100000 0 @@ -104,9 +79,9 @@ tail(RS_early) | chr22 | 51250000 | 51300000 | 0.000 | 0.000 | -#### calculateS50(rs_assay): +#### Compute the replication timing (S50) : -This function returns a dataframe composed of genomic coordinates associated with replication timing as an S50 value comprised within 0 (early replicating) and 1 (late replicating). +The function *calculateS50(rs_assay)* returns a dataframe composed of genomic coordinates associated with replication timing as an S50 [(Chen et al. (2010))](https://doi.org/10.1101/gr.098947.109) value comprised within 0 (early replicating) and 1 (late replicating). ```{r} @@ -138,12 +113,9 @@ print(temp_S50) | chr1 | 5000 | 6000 | 0.250 | | chr1 | 6000 | 7000 | 0.125 | +# Compare the total replication among Repli-Seq assays : -#### calculateURI(rs_x, rs_y): - -This function calculates URI between two Repli-seq assays. It returns a dataframe with the following columns: -chr,start,stop,sum_x,sum_y,mean_xy,URI - +As introduced in [Brison,.O, El-Hilali,S. et al. (2019)](https://doi.org/10.1038/s41467-019-13674-5), Repli-Seq assays could be compared to quantitatively assess which parts of DNA were the most affected by Aphidicolin. The function *calculateURI()* calculates this Under Replication Index (URI) from two Repli-Seq assays loaded with *readRS()*. ```{r} ####### load second Repli-seq assay for comparison @@ -180,4 +152,22 @@ tail(aph_nt_uri) | chr22 | 51150000 | 51200000 | 32.394 | 26.028 | 29.211 | 1.24529116 | | chr22 | 51200000 | 51250000 | 10.063 | 8.533 | 9.298 | 0.82273039 | | chr22 | 51250000 | 51300000 | 0.000 | 0.000 | 0.000 | NaN | + + +## Getting help : + +Need help, Identified a bug, or want to see other features implemented ? +Feel free to open an issue here or send an email to the authors : + +[Sami EL HILALI](mailto:elhilali.sami@gmail.com) and [Chunlong CHEN](mailto:chunlong.chen@curie.fr) + + +## References: + +Brison O., El-Hilali S., Azar, D., Koundrioukoff1 S., Schmidt M., Naehse-Kumpf V., Jaszczyszyn Y., Lachages A.M., Dutrillaux B., Thermes C., Debatisse M. and Chen C.L. (2019) [Transcription-Mediated Organization of the Replication Initiation Program Across Large Genes Sets Up Common Fragile Sites Genome-Wide.](https://doi.org/10.1038/s41467-019-13674-5) ***Nat. Commun.*** 10, 5693 + +Chen C.L., Rappailles A., Duquenne L., Huvet M., Guilbaud G., Farinelli L, Audit B, d'Aubenton-Carafa Y., Arneodo A., Hyrien O. and Thermes C. (2010) [Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes](https://genome.cshlp.org/content/20/4/447.long). ***Genome. 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b/inst/extdata/output/NT_early-S2.wig.bw deleted file mode 100644 index 0166681..0000000 Binary files a/inst/extdata/output/NT_early-S2.wig.bw and /dev/null differ diff --git a/inst/img/README.md b/inst/img/README.md new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/inst/img/README.md @@ -0,0 +1 @@ + diff --git a/inst/img/Repliseq_logo.png b/inst/img/Repliseq_logo.png new file mode 100644 index 0000000..b584d1a Binary files /dev/null and b/inst/img/Repliseq_logo.png differ diff --git a/man/calculateNoiseRatios.Rd b/man/calculateNoiseRatios.Rd index 00b90c4..2be57a0 100644 --- a/man/calculateNoiseRatios.Rd +++ b/man/calculateNoiseRatios.Rd @@ -4,12 +4,14 @@ \alias{calculateNoiseRatios} \title{Calculate noise ratios} \usage{ -calculateNoiseRatios(rs_assay, rs_control) +calculateNoiseRatios(rs_assay, rs_control, noise_method = "max_density") } \arguments{ \item{rs_assay}{a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx} \item{rs_control}{a Repli-seq control assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S0} + +\item{noise_method}{either "max_density"(default) or "min_downslope"} } \value{ an array with the ratios in the order of rs_assay fractions diff --git a/man/readRS.Rd b/man/readRS.Rd index 2634c1b..aa16ebd 100644 --- a/man/readRS.Rd +++ b/man/readRS.Rd @@ -2,18 +2,29 @@ % Please edit documentation in R/readRS.R \name{readRS} \alias{readRS} -\title{Read Repli-seq assay data (bedgraph format).} +\title{Read Repli-Seq assay data (Bedgraph format).} \usage{ -readRS(paths_data, fractions) +readRS(paths_data = NULL, fraction_names = NULL) } \arguments{ -\item{paths_data}{list of paths to repliseq fractions files} +\item{paths_data}{Array. List of paths to Repli-Seq fractions files} -\item{fractions}{list of fractions names} +\item{fraction_names}{Array. List of fractions names (default = S1, ..., Sn)} } \value{ a dataframe composed of genomic coordinates plus all the specified fractions as for example : chr,start,stop,S1,S2,S3,S4,S5,S6 } \description{ -Bedgraphs with a one line header and with similar organization (same length and sorted) +Read and integrate all Repli-Seq fractions in a single dataframe. +Fractions must be formatted as Bedgraph with a one line header and with similar resolutions. +} +\examples{ +# basic usage of read_RS : + +S1_path <- system.file("extdata", "NT_chr22-s1.bdg", package="RepliSeq") +S2_path <- system.file("extdata", "NT_chr22-s2.bdg", package="RepliSeq") + +my_rs_assay <- readRS(paths_data = c(S1_path , S2_path), + fraction_names = c("S1","S2")) + } diff --git a/man/repliseqCorrPlot.Rd b/man/repliseqCorrPlot.Rd new file mode 100644 index 0000000..3c60ed5 --- /dev/null +++ b/man/repliseqCorrPlot.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/repliseqCorrPlot.R +\name{repliseqCorrPlot} +\alias{repliseqCorrPlot} +\title{Calculate and plot correlation plots.} +\usage{ +repliseqCorrPlot( + rs_assay, + corr_method = "pearson", + ordering = "original", + plottype = "mixed" +) +} +\arguments{ +\item{rs_assay}{a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx} + +\item{corr_method}{character in either "pearson","spearman" or "kendall" to use as a parameter for cor.test function} + +\item{ordering}{a character in either "original","AOE", "FPC", "hclust", "alphabet" to reorder the compared variables (to fill the corrplot() order parameter )} + +\item{plottype}{from corrplot type argument. either "upper", "lower" or "mixed". default = "mixed".} +} +\value{ +a mixed correlation plot +} +\description{ +Calculate and draw a correlation plot from Repli-seq assay (data.frame) see http://www.sthda.com/french/wiki/visualiser-une-matrice-de-correlation-par-un-correlogramme +} diff --git a/man/repliseqDensityPlot.Rd b/man/repliseqDensityPlot.Rd new file mode 100644 index 0000000..2fa731f --- /dev/null +++ b/man/repliseqDensityPlot.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/repliseqDensityPlot.R +\name{repliseqDensityPlot} +\alias{repliseqDensityPlot} +\title{Calculate and plot density plots.} +\usage{ +repliseqDensityPlot( + rs_assay, + stat = "counts", + grided = F, + ncols = 3, + rs_resolution = "50kb" +) +} +\arguments{ +\item{rs_assay}{a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx} + +\item{stat}{"counts" (default) or "density" to use in the stat argument} + +\item{grided}{boolean (default = F) if True then each fraction s displayed on a different panel, otherwise all the fractions are colored in a single panel} + +\item{ncols}{(default = 3) amount of columns when grided == T (see ggplot2 facet_wrap ncol parameter)} + +\item{rs_resolution}{resolution of the rs_assay to display in the labels in the plots. Default equals "50kb"} +} +\value{ +a ggplot object displaying density for the provided repliseq assay +} +\description{ +Calculate and draw a density plot from Repli-seq assay (data.frame) +} diff --git a/vignettes/RepliSeq.Rmd b/vignettes/RepliSeq.Rmd new file mode 100644 index 0000000..7371275 --- /dev/null +++ b/vignettes/RepliSeq.Rmd @@ -0,0 +1,282 @@ +--- +title: "RepliSeq" +author: "Sami El Hilali" +date: "2023/6/8" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{RepliSeq} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + + +# Loading a Repli-Seq assay with readRS() : + +This functions reads Repli-seq assays from multiple files (one file for one fraction) and outputs a dataframe from it. +It requires bedgraph inputs with a one line header listing options, with **no other comments** such as : [(bedgraph spec)](http://genome.ucsc.edu/goldenPath/help/bedgraph.html) +track type=bedGraph name=NT_chr22-s1 description=50kbprofile +chr22 0 50000 0 +chr22 50000 100000 0 + +All Bedgraph must have the same resolution (size of genomic windows). + +```{r} +library(RepliSeq) +``` + + +```{r} + +### arguments : +S1_path <- system.file("extdata", "NT_chr22-s1.bdg", package="RepliSeq") +S2_path <- system.file("extdata", "NT_chr22-s2.bdg", package="RepliSeq") +S3_path <- system.file("extdata", "NT_chr22-s3.bdg", package="RepliSeq") +S4_path <- system.file("extdata", "NT_chr22-s4.bdg", package="RepliSeq") +S5_path <- system.file("extdata", "NT_chr22-s5.bdg", package="RepliSeq") +S6_path <- system.file("extdata", "NT_chr22-s6.bdg", package="RepliSeq") +S0_path <- system.file("extdata", "NT_chr22-s0.bdg", package="RepliSeq") + +rs_fractions <- c("S1","S2","S3","S4","S5","S6") + +### Load a 2 fractions Repli-Seq assay +RS_early <- readRS(c(S1_path,S2_path), + rs_fractions[1:2]) +tail(RS_early) + +### Load a 6 fractions Repli-Seq assay +RS_all <- readRS(c(S1_path,S2_path,S3_path,S4_path,S5_path,S6_path), + rs_fractions) +tail(RS_all) + +### 1 fraction RepliSeq ( for controls ) +RS_S0 <- readRS(S0_path,"S0") +tail(RS_S0) + +``` + +# Adapting the resolution of the assay with rescaleRS() : + +This functions rescales Repli-seq assays loaded with readRS to lower resolution ( e.g. from 1kb windows to 50kb windows or 100kb) + +```{r} + +# To rescale from 50kb to 100kb the scale_factor is 2 ( from 1kb to 50kb it would be 50) + +RS_all_100kb <- rescaleRS(RS_all,scale_factor = 2) + +tail(RS_all_100kb) + +``` + +# Generating overlapping windows with smoothRS(rs_assay,scale_factor) : + +This functions rescales Repli-seq assays loaded with readRS to lower resolution ( e.g. from 1kb windows to 50kb windows or 100kb) + +```{r} + +# To get 50kb smoothed profiles from 1kb adjacent profiles +# smooth_factor = 50 --> results in count matrices with genomic windows +# having a step = 1kb and a span of 50kb. +# From 50kb to 100kb the smooth_factor is 2 + +RS_all_100kb <- smoothRS(RS_all,smooth_factor = 2) +tail(RS_all_100kb) + +``` + +# Normalization : + +### Normalize the fractions with normalizeRS() and weight_phases(): + +This function takes as input a Repli-Seq assay loaded with *readRS()* and an array of ratios. +The normalized fractions returned are the fractions divided by the provided ratios. + +```{r} +# Normalizing to a fixed total : +# Compute ratios for a sum == 2000 : + +norm_ratios <- c(sum(RS_all$S1) / 2000, + sum(RS_all$S2) / 2000, + sum(RS_all$S3) / 2000, + sum(RS_all$S4) / 2000, + sum(RS_all$S5) / 2000, + sum(RS_all$S6) / 2000) + +RS_all_normlized <- normalizeRS(RS_all,norm_ratios) + +tail(RS_all_normlized) + +# Use weight_phases() to take into account the FACS gates : +# calculate a normalization factor for each phase based on the experimental FACS profile and a simulation of S-phase progressio (Percentage of replicated DNA, Number of active forks): +gates_df <- data.frame(start=c(24.2519169380677, + 27.282955036018755, + 30.61406625807228, + 34.19265411124849, + 37.47504529876629, + 40.60739992423285), + end=c(27.282955036018755, + 30.61406625807228, + 34.19265411124849, + 37.47504529876629, + 40.60739992423285, + 47.27059148295092)) + +norm_ratios <- weight_phases(rs_assay = RS_all, + G1_peak = 24.15, + G2_peak = 44.2, + gates = gates_df, + TotalReads = 2000*6 ) + +print(norm_ratios) + + +``` + + + +# Compute the replication timing S50 with calculateS50() : + +This functions takes a Repli-Seq assay as input and computes the replication timing as the S50 value [(Chen et al. (2010)](https://doi.org/10.1101/gr.098947.109). This value is comprised between 0 (early replicating) and 1 (late replicating). + +```{r} + +temp_rs <- data.frame(chr = rep("chr1",7), + start = seq(0,6000,1000), + stop = seq(1000,7000,1000), + S1 = c(0,0,0,1,1,1,1), + S2 = c(0,0,1,1,1,1,0), + S3 = c(0,1,1,1,1,0,0), + S4 = c(1,1,1,1,0,0,0)) + + +temp_S50 <- calculateS50(temp_rs) +print(temp_S50) + +``` + + +# calculateURI(rs_x, rs_y) : + +This functions calculates URI between two Repli-seq assays [(Brison,O.,El-Hilali,S. et al. (2019))](https://doi.org/10.1038/s41467-019-13674-5). +It returns a dataframe with the following columns : +chr,start,stop,sum_x,sum_y,mean_xy,URI + + +```{r} +####### load second Repli-seq assay for comparison : +### arguments : + +### load Non treated samples : +S1_path <- system.file("extdata", "NT_chr22-s1.bdg", package="RepliSeq") +S2_path <- system.file("extdata", "NT_chr22-s2.bdg", package="RepliSeq") +S3_path <- system.file("extdata", "NT_chr22-s3.bdg", package="RepliSeq") +S4_path <- system.file("extdata", "NT_chr22-s4.bdg", package="RepliSeq") +S5_path <- system.file("extdata", "NT_chr22-s5.bdg", package="RepliSeq") +S6_path <- system.file("extdata", "NT_chr22-s6.bdg", package="RepliSeq") +S0_path <- system.file("extdata", "NT_chr22-s0.bdg", package="RepliSeq") + +rs_fractions <- c("S1","S2","S3","S4","S5","S6") + +NT <- readRS(paths_data = c(S1_path,S2_path,S3_path,S4_path,S5_path,S6_path), + fraction_names = rs_fractions) + +NT <- normalizeRS(rs_assay = NT, + norm_ratios = c(sum(NT$S1) / 2000, + sum(NT$S2) / 2000, + sum(NT$S3) / 2000, + sum(NT$S4) / 2000, + sum(NT$S5) / 2000, + sum(NT$S6) / 2000)) + +# load and normalize samples treated with Aphidicolin : +S1_path <- system.file("extdata", "Aph_chr22-s1.bdg", package="RepliSeq") +S2_path <- system.file("extdata", "Aph_chr22-s2.bdg", package="RepliSeq") +S3_path <- system.file("extdata", "Aph_chr22-s3.bdg", package="RepliSeq") +S4_path <- system.file("extdata", "Aph_chr22-s4.bdg", package="RepliSeq") +S5_path <- system.file("extdata", "Aph_chr22-s5.bdg", package="RepliSeq") +S6_path <- system.file("extdata", "Aph_chr22-s6.bdg", package="RepliSeq") + + +Aph <- readRS(c(S1_path,S2_path,S3_path,S4_path,S5_path,S6_path), + fraction_names = rs_fractions) + +Aph <- normalizeRS(rs_assay = Aph, + norm_ratios = c(sum(Aph$S1) / 2000, + sum(Aph$S2) / 2000, + sum(Aph$S3) / 2000, + sum(Aph$S4) / 2000, + sum(Aph$S5) / 2000, + sum(Aph$S6) / 2000)) +####### + +aph_nt_uri <- calculateURI(rs_x = Aph, + rs_y = NT) + +tail(aph_nt_uri) + +``` + + +# Remove noise with calculateNoiseRatios() and removeNoise() : + +```{r} + +# compute ratios : +ratios_all <- calculateNoiseRatios(RS_all, RS_S0) +print(ratios_all) + +# use the ratios and the control (S0) to remove noise : +RS_noise_rm_all <- removeNoise(rs_assay = RS_all, + rs_control = RS_S0, + noise_ratios = ratios_all) + +tail(RS_noise_rm_all) + +``` + +# doubleXchr(rs_assay) : + +This function can be used to double the values in count matrices at chrX as for example when normalization haven't been performed on raw data from human male samples. + +```{r} + +RS_all_doubledX <- doubleXchr(RS_all,chr = "chr22") # default chr parameter is "chrX" +tail(RS_all_doubledX) + + +``` + +# Export files with writeBedgraph() and writeBigwig() : + +**(writeBigwig() requires [wigToBigWig](https://www.encodeproject.org/software/wigtobigwig/) installed on the system)**. +This function writes Bigwig profiles for all the fractions of a provided Repli-seq assay. It requires UCSC's WigToBigWig installed to convert from Wiggle to BigWig. + +```{r} + +# Write all to Bedgraph : + +# writeBedgraph(rs_assay = RS_all, +# path_file = "../inst/extdata/output", +# sample_name = "NT_all") + +# Write all as BigWig : + +# writeBigwig(rs_assay = RS_all, +# path_file = "../inst/extdata/output", +# sample_name = "NT_all", +# chromsizes = "../inst/extdata/Hg19/chromsizes.txt", +# wiggle_start = 1, +# wiggle_step = 50000, +# wiggle_span = 50000) + +``` + + + diff --git a/vignettes/how-to-use.Rmd b/vignettes/how-to-use.Rmd deleted file mode 100644 index 83a4a2d..0000000 --- a/vignettes/how-to-use.Rmd +++ /dev/null @@ -1,320 +0,0 @@ ---- -title: "how-to-use" -output: rmarkdown::html_vignette -vignette: > - %\VignetteIndexEntry{how-to-use} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} ---- - -```{r, include = FALSE} -knitr::opts_chunk$set( - collapse = TRUE, - comment = "#>" -) -``` - -```{r setup} -library(RepliSeq) -``` - -# readRS(paths_data,fractions) : - -This functions reads Repli-seq assays from multiple files (one file for one fraction) and outputs a dataframe from it. -It requires bedgraph inputs with a one line header listing options, with **no other comments** such as : [(bedgraph spec)](http://genome.ucsc.edu/goldenPath/help/bedgraph.html) -track type=bedGraph name=NT_chr22-s1 description=50kbprofile -chr22 0 50000 0 -chr22 50000 100000 0 - -```{r} - -### args : -temp_paths <- c("../inst/extdata/NT_chr22-s1.bdg","../inst/extdata/NT_chr22-s2.bdg", - "../inst/extdata/NT_chr22-s3.bdg","../inst/extdata/NT_chr22-s4.bdg", - "../inst/extdata/NT_chr22-s5.bdg","../inst/extdata/NT_chr22-s6.bdg") -temp_fractions <- c("S1","S2","S3","S4","S5","S6") - -### 2 fractions RepliSeq -# apply function : -RS_early <- readRS(temp_paths[1:2],temp_fractions[1:2]) -# outputs : -tail(RS_early) -typeof(RS_early) -summary(RS_early) - -### 6 fractions RepliSeq -# apply function : -RS_all <- readRS(temp_paths,temp_fractions) -# outputs : -tail(RS_all) - -### 1 fraction RepliSeq ( for S0 controls ) -# apply function : -RS_S0 <- readRS("../inst/extdata/NT_chr22-s0.bdg","S0") -# outputs : -tail(RS_S0) - -``` - -# rescaleRS(rs_assay,scale_factor) : - -This functions rescales Repli-seq assays loaded with readRS to lower resolution ( e.g. from 1kb windows to 50kb windows or 100kb) - -```{r} - -# To rescale from 50kb to 100kb the scale_factor is 2 ( from 1kb to 50kb it would be 50) - -### 2 fractions RepliSeq -# apply function : -RS_early_100kb <- rescaleRS(RS_early,2) -# outputs : -tail(RS_early_100kb) - -### 6 fractions RepliSeq -# apply function : -RS_all_100kb <- rescaleRS(RS_all,2) -# outputs : -tail(RS_all_100kb) - -### 1 fraction RepliSeq ( for S0 controls ) -# apply function : -RS_S0_100kb <- rescaleRS(RS_S0,2) -# outputs : -tail(RS_S0_100kb) - -``` - -# smoothRS(rs_assay,scale_factor) : - -This functions rescales Repli-seq assays loaded with readRS to lower resolution ( e.g. from 1kb windows to 50kb windows or 100kb) - -```{r} - -# To get 50kb smoothed profiles from 1kb adjacent profiles smooth_factor = 50 --> results in count matrices with -# genomic windows having a step = 1kb and a span of 50kb. -# From 50kb to 100kb the smooth_factor is 2 - -### 2 fractions RepliSeq -# apply function : -RS_early_smoothed_2 <- smoothRS(RS_early,2) -# outputs : -tail(RS_early_smoothed_2) - -### 6 fractions RepliSeq -# apply function : -RS_all_100kb <- rescaleRS(RS_all,2) -# outputs : -tail(RS_all_100kb) - -### 1 fraction RepliSeq ( for S0 controls ) -# apply function : -RS_S0_100kb <- rescaleRS(RS_S0,2) -# outputs : -tail(RS_S0_100kb) - -``` - -# weight_phases(rs_assay, G1_peak,G2_peak,gates,SimSPhase=NA,TotalReads=NA) : - -```{r} - -### 6 fractions RepliSeq -# calculate a normalization factor for each phase based on the experimental FACS profile and a simulation of S-phase progressio (Percentage of replicated DNA, Number of active forks): -norm_ratios <- weight_phases(rs_assay = RS_all, - G1_peak = 24.15, - G2_peak = 44.2, - gates = data.frame( start=c(24.2519169380677,27.282955036018755,30.61406625807228,34.19265411124849,37.47504529876629,40.60739992423285), - end=c(27.282955036018755,30.61406625807228,34.19265411124849,37.47504529876629,40.60739992423285,47.27059148295092)), - TotalReads = 2000*6 ) - -print(norm_ratios) - -``` - -# normalizeRS(rs_assay,norm_ratios) : - -```{r} -### 6 fractions RepliSeq -# As alternative to the use of weight_phases -# 1st calculate ratios for a sum == 2000 : -norm_ratios <- c(sum(RS_all$S1) / 2000, - sum(RS_all$S2) / 2000, - sum(RS_all$S3) / 2000, - sum(RS_all$S4) / 2000, - sum(RS_all$S5) / 2000, - sum(RS_all$S6) / 2000) - -# apply normalizeRS: -RS_all_normlized<- normalizeRS(RS_all,norm_ratios) -# outputs : -tail(RS_all_normlized) - -``` - - - -# calculateS50(rs_assay) : - -```{r} - -temp_rs <- data.frame(chr = rep("chr1",7), - start = seq(0,6000,1000), - stop = seq(1000,7000,1000), - S1 = c(0,0,0,1,1,1,1), - S2 = c(0,0,1,1,1,1,0), - S3 = c(0,1,1,1,1,0,0), - S4 = c(1,1,1,1,0,0,0)) - - -temp_S50 <- RepliSeq::calculateS50(temp_rs) -print(temp_S50) - -### 2 fractions RepliSeq -# apply function : -temp.S50 <- RepliSeq::calculateS50(RS_early) -# outputs : -tail(temp.S50) - -### 6 fractions RepliSeq -# apply function : -temp.S50 <- RepliSeq::calculateS50(RS_all) -# outputs : -tail(temp.S50) -summary(temp.S50$S50) - -``` - - -# calculateURI(rs_x, rs_y) : - -This functions calculates URI between two Repli-seq assays. It returns a dataframe with the following columns : -chr,start,stop,sum_x,sum_y,mean_xy,URI - - -```{r} -####### load second Repli-seq assay for comparison : -### args : -aph_paths <- c("../inst/extdata/Aph_chr22-s1.bdg","../inst/extdata/Aph_chr22-s2.bdg", - "../inst/extdata/Aph_chr22-s3.bdg","../inst/extdata/Aph_chr22-s4.bdg", - "../inst/extdata/Aph_chr22-s5.bdg","../inst/extdata/Aph_chr22-s6.bdg") -aph_fractions <- c("S1","S2","S3","S4","S5","S6") - -# read : -RS_aph_all <- readRS(aph_paths,aph_fractions) -RS_aph_early <- readRS(aph_paths[1:2],aph_fractions[1:2]) -####### - -### 2 fractions RepliSeq -# apply function : -aph_nt_uri <- calculateURI(RS_aph_early,RS_early) -# outputs : -tail(aph_nt_uri) - -### 6 fractions RepliSeq -# apply function : -aph_nt_uri <- calculateURI(RS_aph_all,RS_all) -# outputs : -tail(aph_nt_uri) - - - -``` - - -# calculateNoiseRatios(rs_assay, rs_control) : - -```{r} - -### 2 fractions RepliSeq -# apply function : -ratios_early <- calculateNoiseRatios(RS_early, RS_S0) -# outputs : -print(ratios_early) - -### 6 fractions RepliSeq -# apply function : -ratios_all <- calculateNoiseRatios(RS_all, RS_S0) -# outputs : -print(ratios_all) - -``` - -# removeNoise(rs_assay, rs_control, noise_ratios) : - -```{r} - -### 2 fractions RepliSeq -# apply function : -RS_noise_rm_early <- removeNoise(RS_early, RS_S0,ratios_early) -# outputs : -tail(RS_noise_rm_early) - -### 6 fractions RepliSeq -# apply function : -RS_noise_rm_all <- removeNoise(RS_all, RS_S0,ratios_all) -# outputs : -tail(RS_noise_rm_all) - -``` - -# doubleXchr(rs_assay) : - -This function can be used to double the values in count matrices at chrX as for example when normalization haven't been performed on raw data from human male samples. - -```{r} - -### 2 fractions RepliSeq -# apply function : -RS_early_doubledX <- doubleXchr(RS_early,chr = "chr22") # default chr parameter is "chrX" -# outputs : -tail(RS_early_doubledX) - -### 6 fractions RepliSeq -# apply function : -RS_all_doubledX <- doubleXchr(RS_all,chr = "chr22") # default chr parameter is "chrX" -# outputs : -tail(RS_all_doubledX) - -### 1 fraction RepliSeq (for S0 controls) -# apply function : -RS_S0_doubledX <- doubleXchr(RS_S0,chr = "chr22") # default chr parameter is "chrX" -# outputs : -tail(RS_S0_doubledX) - -``` - -# writeBedgraph(rs_assay,path_file,sample_name) : - -```{r} - -### 2 fractions RepliSeq -writeBedgraph(RS_early,"../inst/extdata/output","NT_early") - -### 6 fractions RepliSeq -writeBedgraph(RS_all,"../inst/extdata/output","NT_all") - -### 1 fraction RepliSeq (for S0 controls) -writeBedgraph(RS_S0,"../inst/extdata/output","NT") - -``` - - -# writeBigwig(rs_assay,path_file,sample_name,chromsizes,wiggle_start,wiggle_step_wiggle_span) : - -**(requires [wigToBigWig](https://www.encodeproject.org/software/wigtobigwig/) installed on the system)**. -This function writes Bigwig profiles for all the fractions of a provided Repli-seq assay. It requires UCSC's WigToBigWig installed to convert from Wiggle to BigWig. - -```{r} - -### 2 fractions RepliSeq -writeBigwig(RS_early,"../inst/extdata/output","NT_early","../inst/extdata/Hg19/chromsizes.txt",wiggle_start = 1,wiggle_step = 50000, wiggle_span = 50000) - -### 6 fractions RepliSeq -writeBigwig(RS_all,"../inst/extdata/output","NT_all","../inst/extdata/Hg19/chromsizes.txt",wiggle_start = 1,wiggle_step = 50000, wiggle_span = 50000) - -### 1 fraction RepliSeq (for S0 control) -writeBigwig(RS_S0,"../inst/extdata/output","NT","../inst/extdata/Hg19/chromsizes.txt",wiggle_start = 1,wiggle_step = 50000, wiggle_span = 50000) - -``` - -