detectERCCreads: detectERCCreads

In EngeLab/RNAseqFunctions: RNA sequencing functions for the Enge lab

Description

Detects the 92 ERCC reads in the rownames of the counts data.frame. ERCC reads must be named with the standard naming convention that matches the regex "^ERCC\-[0-9]*$".

Arguments

counts	data.frame; A data frame with counts data with gene names as rownames.
regex	Regular expression to extract ERCC reads.
warn	Logical indicating if a warning should be issued if < 92 ERCC reads are detected.

Value

A logical vector with length = nrow(counts) that is TRUE when the counts data.frame row contains an ERCC read. A warning is issued if all 92 ERCC reads are not detected.

Author(s)

Jason Serviss

Examples

counts <- data.frame(runif(100), row.names = c(1:8, paste0("ERCC-", 1:92)))
detectERCCreads(counts)

EngeLab/RNAseqFunctions documentation built on May 5, 2019, 9:43 p.m.