filterExpression: Filter expression

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Filter expression

Description

To filter out non expressed genes this method uses the FPKM values to get a comparable value over genes. For each gene, if the pth- percentile is greater than the fpkmCutoff value, it passes the filter. To calcute the FPKM values the user needs to provide a GTF file or the basepair parameter as described in fpkm.

Usage

filterExpression(object, ...)

## S4 method for signature 'OutriderDataSet'
filterExpression(
  object,
  gtfFile,
  fpkmCutoff = 1,
  percentile = 0.95,
  filterGenes = TRUE,
  savefpkm = FALSE,
  minCounts = FALSE,
  addExpressedGenes = TRUE,
  ...
)

Arguments

object	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
percentile	a numeric indicating the percentile FPKM value to compare against the fpkmCutoff
filterGenes	If TRUE, the default, the object is subseted.
savefpkm	If TRUE, the FPKM values are saved as assay
minCounts	If TRUE, only genes with 0 counts in all samples are filtered
addExpressedGenes	If TRUE (default), adds 5 columns to the colData with information regarding the number of expressed genes per sample

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)

gagneurlab/OUTRIDER documentation built on April 29, 2024, 2:22 a.m.