filterExpression {OUTRIDER} | R Documentation |
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
.
filterExpression(x, ...) ## S4 method for signature 'OutriderDataSet' filterExpression(x, gtfFile, fpkmCutoff = 1, percentile = 0.95, filterGenes = TRUE, savefpkm = FALSE, minCounts = FALSE, addExpressedGenes = TRUE, ...)
x |
An OutriderDataSet object |
... |
Additional arguments passed to |
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 |
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
|
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.
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)