Skip to content

Update to Genotype Table Generation #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
skitchen19 wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update to Genotype Table Generation #8

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 8 additions & 8 deletions tools/corals/coral_multilocus_genotype/coral_multilocus_genotype.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -776,7 +776,9 @@ prep_genotype_tibble <- id_data_table %>%
mutate(coral_mlg_rep_sample_id=ifelse(is.na(coral_mlg_rep_sample_id.x),coral_mlg_rep_sample_id.y,coral_mlg_rep_sample_id.x)) %>%
ungroup() %>%
dplyr::select(-coral_mlg_rep_sample_id.x,-coral_mlg_rep_sample_id.y, -group.x,-group.y) %>%
distinct();
group_by(coral_mlg_clonal_id) %>%
arrange(coral_mlg_rep_sample_id) %>%
slice(1);

# Confirm that the representative mlg is the same between runs.
uniques2 <- unique(prep_genotype_tibble[c("group", "coral_mlg_rep_sample_id")]);
Expand All @@ -796,18 +798,17 @@ prep_genotype_tibble$coral_mlg_rep_sample_id[na.mlg3] <- uniques2$coral_mlg_rep_
representative_mlg_tibble <- prep_genotype_tibble %>%
mutate(coral_mlg_rep_sample_id=ifelse(is.na(coral_mlg_rep_sample_id) & (db_match =="no_match"), affy_id, coral_mlg_rep_sample_id)) %>%
ungroup() %>%
select(-group)%>%
distinct();
select(-group);
# prep_genotype_table_tibble looks like this:
# affy_id coral_mlg_clonal_id user_specimen_id db_match
# a550962...CEL HG0120 1090 match
# genetic_coral_species_call coral_mlg_rep_sample_id
# A.palmata 1104
prep_genotype_table_tibble <- stag_db_report %>%
select("affy_id", "coral_mlg_clonal_id", "user_specimen_id", "db_match", "genetic_coral_species_call") %>%
left_join(representative_mlg_tibble %>%
select("affy_id", "coral_mlg_rep_sample_id"),
by='affy_id');
left_join(representative_mlg_tibble %>%
select("coral_mlg_rep_sample_id", "coral_mlg_clonal_id"),
by='coral_mlg_clonal_id');
# genotype_table_tibble looks like this:
# affy_id coral_mlg_clonal_id user_specimen_id db_match
# a550962-436.CEL HG0120 1090 match
Expand All @@ -816,8 +817,7 @@ prep_genotype_table_tibble <- stag_db_report %>%
genotype_table_tibble <- prep_genotype_table_tibble %>%
left_join(affy_metadata_data_frame %>%
select("user_specimen_id", "bcoral_genet_id"),
by='user_specimen_id') %>%
drop_na(coral_mlg_rep_sample_id);
by='user_specimen_id');
write_data_frame(output_data_dir, "genotype.tabular", genotype_table_tibble);

# Output the file needed for populating the person table.
Expand Down