write_deseq: Write DESeq results

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Write DESeq results

Description

Write DESeq result files, raw counts, rlog values, normalized counts to an Excel file.

Usage

write_deseq(
  result_all,
  dds,
  rld,
  biomart,
  sets,
  fpkm,
  text_files = FALSE,
  cutoff,
  file = "DESeq.xlsx",
  overwrite = TRUE,
  ...
)

Arguments

result_all	a list from results_all
dds	a DESeqDataset object with count tables
rld	a DESeqTransform obect with rlog values
biomart	annotations from read_biomart
sets	table with set intersections, optional
fpkm	matrix of fpkm values, optional
text_files	write results to separate txt files, mainly for IPA input
cutoff	if text_files is TRUE, only write genes below this p-value cutoff
file	file name
overwrite	overwrite existing Excel file. Default is FALSE.
...	additional options passed to annotate_results

Value

A tibble

Author(s)

Chris Stubben

Examples

## Not run: 
 write_deseq(res, dds, rld, human98)

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on Aug. 20, 2024, 12:22 a.m.