detectLowQualityGenes: detectLowQualityGenes

In jasonserviss/sp.scRNAseqData: Data and processing functions for the CIMseq.data package

Description

In gene expression counts data if can often be the case that some genes are not detected. This can simply be due to the fact that the gene is not expressed in the tissue or, in addition, that the sequencing depth was not sufficient to detect the gene. In addition, some genes may be detected but in so few samples or at such a low level that it makes the quantified value highly unreliable. In these cases, it is desireable to remove the gene before downstream analysis which is facilitated by this function.

Arguments

counts	data.frame; A data frame with counts data with gene names as rownames.
mincount	numeric; A minimum rowSum for which rows with a higher rowSum will be detected. Default = 0.

Value

A logical vector with length = nrow(counts) that is TRUE when the counts data.frame row meets both tested conditions.

Author(s)

Jason Serviss

Examples

counts <- data.frame(c(0, runif(10)), c(0, runif(10)), c(0, runif(10)))
detectLowQualityGenes(counts)

jasonserviss/sp.scRNAseqData documentation built on Jan. 8, 2020, 11:46 a.m.