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. 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(x, ...)

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

### 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
`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)

[Package OUTRIDER version 1.4.2 Index]