TEnGExA-package {TEnGExA} R Documentation

Tissue Enrichment analysis of any number of genes with any number of tissues, irrespective of any organism provided only the read count matrix or FPKM value matrix.

While working on transcripts such as CDS, alternative splicing, circular RNAs or lncRNAs, one can annotate them to assign some biological process or functions to relate with some specific pathway or network analysis. But while dealing with data from multiple tissues it is always preferable to proceed with some tissue-specific or tissue-enriched transcripts only. Recently tools have been developed for tissue-enrichment analysis but not only needs technical advancement to work with but more importantly limited to specific organism or predetermined list of genes or transcripts. This R package (TEnGExA) has been developed to perform tissue-enrichment analysis of any number of genes with any number of tissues, irrespective of any organism provided only the read count matrix or FPKM value matrix.

Required software and packages:

R (http://www.r-project.org/)

Command

result=TEnGExA(x, fpkm_flag=0, threshold=5, tissue_num=5, min_fpkm= 1)

Parameters

Count matrix or FPKM matrix

x - could be a count matrix with following columns:

1st column: Gene/Transcript Id, 2nd column: Gene/Transcript Length, 3rd ... nth columns are read counts of genes/transcripts in different tissues/samples

x - could be a fpkm values matrix with following columns:

1st column: Gene/Transcript Id, 2nd ... nth columns are fpkm values of genes/transcripts in different tissues/samples

fpkm_flag

fpkm_flag - 0 for count matrix or 1 for FPKM value matrix; Default-value 0

threshold

threshold - fpkm value threshold to be considered for calling any gene/transcript as expressed; Default-value 5

tissue_num

tissue_num - Minimum number of tissues to be considered for assigning group enrichment class; Default-value 5

min_fpkm

min_fpkm - Minimum FPKM value threshold to be considered for expression analysis; Default-value 1

Output

The output results are in matrix form with details in last column; Default-output-file output1.csv

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Author(s)

Hukam C Rawal, Angadi U B, T. K. Mondal.

Original code written by : Angadi U B Angadi UB angadiub@gmail.com

Updated and debugged by: Hukam C. Rawal

Citation:

Rawal, H.C., Angadi, U., Mondal, T.K. (2021). TEnGExA: an R package based tool for tissue enrichment and gene expression analysis. Briefings in Bioinformatics, 22(3):bbaa221. https://doi.org/10.1093/bib/bbaa221

KEYWORDS

Tissue Enriched, Tissue Enhanced, Gene, Tissue, read count, FPKM

How to run:

Install package:

Directly from github

remotes::install_github("hcrawal/TEnGExA")

Using source code

1. Download TEnGExA_*.tar.gz file

2. Open Rstudio or R and type as below:

install.packages("~/TEnGExA_*.tar.gz", repos = NULL, type = "source")

Call library

library('TEnGExA')

Run with sample file

datafile= paste(path.package("TEnGExA"),"/exdata/sample-fpkm-matrix-1.csv",sep="")

{or if specifying your input file path: datafile= paste("file_path/matrix_file_name",sep="") }

data1 = read.csv(datafile, header = TRUE)

result=TEnGExA(data1, fpkm_flag=1, threshold=5, tissue_num= 4, min_fpkm= 1)

write.csv(result, "output1.csv")