make_limma_tables: Writes out the results of a limma search using toptable().

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

Writes out the results of a limma search using toptable().

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 toptable() output in separate .csv files and/or sheets in excel 3. Since I have been using qvalues a lot for other stuff, add a column for them.

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 toptable() output in separate .csv files and/or sheets in excel 3. Since I have been using qvalues a lot for other stuff, add a column for them.

Usage

make_limma_tables(
  fit = NULL,
  adjust = "BH",
  n = 0,
  coef = NULL,
  annot_df = NULL,
  intercept = FALSE
)

make_limma_tables(
  fit = NULL,
  adjust = "BH",
  n = 0,
  coef = NULL,
  annot_df = NULL,
  intercept = FALSE
)

Arguments

fit	Result from lmFit()/eBayes()
adjust	Pvalue adjustment chosen.
n	Number of entries to report, 0 says do them all.
coef	Which coefficients/contrasts to report, NULL says do them all.
annot_df	Optional data frame including annotation information to include with the tables.
intercept	Intercept model?

Value

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

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

See Also

[limma] [write_xlsx()]

[limma] [write_xlsx()]

Examples

## Not run: 
 finished_comparison = eBayes(limma_output)
 table = make_limma_tables(finished_comparison, adjust = "fdr")

## End(Not run)
## Not run: 
 finished_comparison = eBayes(limma_output)
 table = make_limma_tables(finished_comparison, adjust = "fdr")

## End(Not run)

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