Remove low count genes

Source: R/fct_normalisation.R

Removes genes having a sum of counts accross all samples lesser than the specified threshold. It returns un aupdated TCC object, which count element contains the filtered expression matrix.

filter_low_counts(tcc, thr)

Arguments

tcc

data to be filtered to remove low count genes
thr

the sum of counts across all samples to be exceeded for a gene

Value

a TCC-Class object

Examples

data("abiotic_stresses")
tcc_object <- DIANE::normalize(abiotic_stresses$raw_counts, 
abiotic_stresses$conditions, iteration = FALSE)
threshold = 10*length(abiotic_stresses$conditions)
tcc_object <- DIANE::filter_low_counts(tcc_object, threshold)
normalized_counts <- TCC::getNormalizedData(tcc_object)