plotLowQualityCells: plotLowQualityCells

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

Description

Plots histograms of the two metrics evaluated by the detectLowQualityCells function.

Usage

plotLowQualityCells(counts, mincount = 4e+05, geneName = "ACTB",
  quantileCut = 0.01)

Arguments

counts	data.frame; A data frame with counts data with gene names as rownames and sample names as colnames.
mincount	numeric; A minimum colSum for which columns with a higher colSum will be detected. Default = 4e5.
geneName	character; The gene name to use for the quantile cutoff. This must be present in the rownames of the counts argument. Default is ACTB.
quantileCut	numeric; This indicates probability at which the quantile cutoff will be calculated using the normal distribution. Default = 0.01.

Value

A tibble containing the plot data.

Author(s)

Jason T. Serviss

Examples

c <- moveGenesToRownames(testingCounts)[1:12, ]
detectLowQualityCells(c, geneName = "ACTB", mincount = 30)

martinenge/RNAseqFunctions documentation built on May 28, 2019, 3:10 p.m.