filterLowCountGenes: Filter genes from a TCC-class object

In TCC: TCC: Differential expression analysis for tag count data with robust normalization strategies

Description

This function takes a TCC object and returns a new TCC object without genes having low count tags across samples. The threshold is configurable with low.count parameter.

Usage

filterLowCountGenes(tcc, low.count = 0)

Arguments

tcc	TCC-class object.
low.count	numeric value (>= 0) specifying the threshold for filtering genes. The higher value indicates the more numbers of genes to be filtered out.

Value

TCC-class object consisting of genes whose total counts across samples is higher than the low.count value.

Examples

# Filtering genes with zero counts across samples (default) from
# a hypothetical count dataset that originally has 1,000 genes.
data(hypoData)
group <- c(1, 1, 1, 2, 2, 2)
tcc <- new("TCC", hypoData, group)
dim(tcc$count)
tcc <- filterLowCountGenes(tcc)
dim(tcc$count)

# Filtering genes with 10 counts across samples from hypoData.
data(hypoData)
group <- c(1, 1, 1, 2, 2, 2)
tcc <- new("TCC", hypoData, group)
dim(tcc$count)
tcc <- filterLowCountGenes(tcc, 10)
dim(tcc$count)

TCC documentation built on Nov. 8, 2020, 8:20 p.m.