write_all_de_results: Write differentially expressed gene data for multiple result...

In DEVis: A Differential Expression Analysis Toolkit for Visual Analytics and Data Aggregation

Description

This function accepts a list of DE result sets and writes their outputs individually to file. Relies on init_cutoffs() significance thresholds. Filenames will be generated automatically based on the contrasts performed during the results() function. Output will be written to the /DE/data/ folder.

Usage

write_all_de_results(res_list, lfc_filter = FALSE)

Arguments

res_list	A list of DESeq result sets.
lfc_filter	Also impose a filter on the DE set by a minimum absolute log2foldChange as determined by init_cutoffs(). Default=FALSE.

Value

Output for each result set will be written to file This function does not return a value.

See Also

init_cutoffs, create_dir_struct

Examples

## Not run: 

#Prepare a result list for aggregation.
res.day1 <- results(dds, contrast=c("Condition_Time", "day1_disease", "day1_control"))
res.day2 <- results(dds, contrast=c("Condition_Time", "day2_disease", "day2_control"))
res.day3 <- results(dds, contrast=c("Condition_Time", "day3_disease", "day3_control"))
myResList <- list(res.day1, res.day2, res.day3)

#Write differentally expressed gene data for each contrast to file.
#Include a minimum fold change filter. This will output 3 files.
write_all_de_results(res_list=myResList, lfc_filter=TRUE)


## End(Not run)

DEVis documentation built on May 2, 2019, 3:18 p.m.