log2CPM {PathoStat}R Documentation

Compute log2(counts per mil reads) and library size for each sample

Description

Compute log2(counts per mil reads) and library size for each sample

Usage

log2CPM(qcounts, lib.size = NULL)

Arguments

qcounts

quantile normalized counts

lib.size

default is colsums(qcounts)

Value

list containing log2(quantile counts per mil reads) and library sizes

Examples

example_data_dir <- system.file("example/data", package = "PathoStat")
pathoreport_file_suffix <- "-sam-report.tsv"
datlist <- readPathoscopeData(example_data_dir, pathoreport_file_suffix)
countdat <- datlist$countdata
lcpm <- log2CPM(countdat)

[Package PathoStat version 1.4.1 Index]