filterGeneExpr {psichomics}R Documentation

Filter genes based on their expression

Description

Filter genes based on their expression

Usage

filterGeneExpr(geneExpr, minMean = 0, maxMean = Inf, minVar = 0,
  maxVar = Inf, minCounts = 10, minTotalCounts = 15)

Arguments

geneExpr

Data frame or matrix: gene expression

minMean

Numeric: minimum of read count mean per gene

maxMean

Numeric: maximum of read count mean per gene

minVar

Numeric: minimum of read count variance per gene

maxVar

Numeric: maximum of read count variance per gene

minCounts

Numeric: minimum number of read counts per gene for at least some samples

minTotalCounts

Numeric: minimum total number of read counts per gene

Value

Boolean vector indicating which genes have sufficiently large counts

Examples

geneExpr <- readFile("ex_gene_expression.RDS")

# Add some genes with low expression
geneExpr <- rbind(geneExpr, 
                  lowReadGene1=c(rep(4:5, 10)),
                  lowReadGene2=c(rep(5:1, 10)),
                  lowReadGene3=c(rep(10:1, 10)),
                  lowReadGene4=c(rep(7:8, 10)))

# Filter out genes with low reads across samples
geneExpr[filterGeneExpr(geneExpr), ]
[Package psichomics version 1.8.2 Index]