write_de_table: Writes out the results of a single pairwise comparison.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Writes out the results of a single pairwise comparison.

Description

However, this will do a couple of things to make one's life easier: 1. Make a list of the output, one element for each comparison of the contrast matrix. 2. Write out the results() output for them in separate sheets in excel. 3. Since I have been using qvalues a lot for other stuff, add a column.

Usage

write_de_table(data, type = "limma", excel = "de_table.xlsx", ...)

Arguments

data	Output from results().
type	Which DE tool to write.
excel	Filename into which to save the xlsx data.
...	Parameters passed downstream, dumped into arglist and passed, notably the number of genes (n), the coefficient column (coef)

Details

Tested in test_24deseq.R Rewritten in 2016-12 looking to simplify combine_de_tables(). That function is far too big, this should become a template for that.

Value

List of data frames comprising the toptable output for each coefficient, I also added a qvalue entry to these toptable() outputs.

See Also

write_xlsx

Examples

## Not run: 
 finished_comparison <- eBayes(deseq_output)
 data_list <- write_deseq(finished_comparison, workbook="excel/deseq_output.xls")

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.