readFeatureAnnotationForEdgeR: Read feature annotation for EdgeR pipeline

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

Read feature annotation for EdgeR pipeline

Description

Read feature annotation for EdgeR pipeline

Usage

readFeatureAnnotationForEdgeR(featureNames, file = NULL)

Arguments

featureNames	Character string, feature names
file	A tab-delimited file with header that provides feature annotation

Value

A data.frame, with the first column named FeatureName, which are the input feature names. The rest columns contain annotations.

The functions tries to parse feature annotation file if it is present. If not, it will use guessAndAnnotate to annotate the features.

Note that for gene symbols, only human gene symbols are supported.

Examples

anno <- "GeneID\tGeneSymbol\n1234\tCCR5\n1235\tCCR6"
annoFile <- tempfile()
writeLines(anno, annoFile)

featIds <- c("1235", "1234")
## use file
readFeatureAnnotationForEdgeR(featIds, file=annoFile)
## Not run: 
  ## use ribiosAnnotation, depending on database connection
  readFeatureAnnotationForEdgeR(featIds, file=NULL)

## End(Not run)

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