filterExpression {OUTRIDER}R Documentation

Filter expression

Description

To filter out non expressed genes this method uses the FPKM values to get a comparable value over genes. To calcute the FPKM values the user needs to provide a GTF file or the basepair parameter as described in fpkm.

Usage

filterExpression(x, ...)

## S4 method for signature 'OutriderDataSet'
filterExpression(x, gtfFile, fpkmCutoff = 1,
  filterGenes = TRUE, savefpkm = FALSE, minCounts = FALSE, ...)

Arguments

x

An OutriderDataSet object

...

Additional arguments passed to computeGeneLength

gtfFile

A txDb object or a GTF/GFF file to be used as annotation

fpkmCutoff

The threshold for filtering based on the FPKM value

filterGenes

If TRUE, the default, the object is subseted.

savefpkm

If TRUE the FPKM values are saved as assay

minCounts

Filter for required read counts per gene

Value

An OutriderDataSet containing the passedFilter column, which indicates if the given gene passed the filtering threshold. If filterGenes is TRUE the object is already subsetted.

Examples

ods <- makeExampleOutriderDataSet(dataset="GTExSkinSmall")
annotationFile <- system.file("extdata", 
    "gencode.v19.genes.small.gtf.gz", package="OUTRIDER")
ods <- filterExpression(ods, annotationFile, filterGenes=FALSE)

mcols(ods)['passedFilter']
fpkm(ods)[1:10,1:10]
dim(ods)

ods <- ods[mcols(ods)[['passedFilter']]]
dim(ods)


[Package OUTRIDER version 1.0.4 Index]