writeDGEList: Write an DGEList object as plain files for downstream...

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Write an DGEList object as plain files for downstream analysis

Description

Write an DGEList object as plain files for downstream analysis

Usage

writeDGEList(
  dgeList,
  exprs.file,
  fData.file,
  pData.file,
  group.file,
  groupLevels.file,
  feat.name = NULL,
  feat.desc = NULL
)

Arguments

dgeList	An DGEList object
exprs.file	File name where counts are saved
fData.file	File name where feature annotations are saved
pData.file	File name where sample annotations are saved
group.file	File name where the sample group information is saved
groupLevels.file	File where the sample group levels are saved
feat.name	Feature names. Can be a column name in genes of the DGEList object, or a vector of the same length as the fetaures. If NULL, row names of the count matrix are used.
feat.desc	Feature descriptions, used in GCT files. If NULL, 'GeneSymbol' will be used if the column is present, otherwise no description will be used Expression values are saved by default in the gct format, unless the file name ends with tsv in which case a tab-separated value (TSV) file will be saved. Sample group and group level information are derived from the group column of the sample annotation.

Note

In case the input matrix has no feature name, the feature names are set to be the integer array starting from 1.

In case no genes item is available in the DGEList, a minimal data.frame containing one column, Feature, is exported with row names of the count matrix used as both row names as well as the content of the Feature column.

Examples

y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4)
d <- DGEList(counts=y, group=rep(1:2,each=2))

exprsFile <- tempfile()
fDataFile <- tempfile()
pDataFile <- tempfile()
groupFile <- tempfile()
groupLevelsFile <- tempfile()
writeDGEList(d, exprs.file=exprsFile, fData.file=fDataFile, pData.file=pDataFile, 
  group.file=groupFile, groupLevels.file=groupLevelsFile)

head(ribiosIO::read_gct_matrix(exprsFile))
head(ribiosIO::readMatrix(fDataFile))
head(ribiosIO::readMatrix(pDataFile))
head(readLines(groupFile))
head(readLines(groupLevelsFile))

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.