filter_rare: Filter rare and low abundance genes

In BIGslu/RNAetc: RNA-seq Data Cleaning And Analysis

Filter rare and low abundance genes

Description

Filter genes at a minimum counts per million (CPM) in a minmum number or percent of total samples.

Usage

filter_rare(
  dat, 
  min_CPM, 
  gene_var="ensembl_gene_id",
  min_sample=NULL, 
  min_pct=NULL, 
  plot=FALSE,
  #Deprecated
  min.CPM=NULL, 
  gene.var=NULL,
  min.sample=NULL, 
  min.pct=NULL)
)

Arguments

dat	DGEList output by edgeR::DEGList( )
min_CPM	numeric minimum counts per million (CPM)
gene_var	character name for column with gene names in dat$genes that matches names in expression data dat$E. Default "ensembl_gene_id"
min_sample	numeric minimum number of samples
min_pct	numeric minimum percent of samples (0-100)
plot	logical if should plot mean variance trends
min.CPM	Deprecated form of min_CPM
gene.var	Deprecated form of gene_var
min.sample	Deprecated form of min_sample
min.pct	Deprecated form of min_pct

Value

DGEList object filtered to not rare genes

Examples

dat.filter <- filter_rare(dat = example.dat, min_CPM = 0.1, min_sample = 3,
                          gene_var="geneName")
dat.filter <- filter_rare(dat = example.dat, min_CPM = 0.1, min_pct = 10,
                          plot = TRUE, gene_var="geneName")

BIGslu/RNAetc documentation built on Feb. 13, 2025, 7:42 a.m.