convertCounts: Function convertCounts

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Takes a count matrix as input and converts to other desired units. Supported units include CPM, FPKM, FPK and TPM. Output units can be logged and/or normalized. Calculations are performed using edgeR functions except for the conversion to TPM which is converted from FPKM using the formula provided by [Harold Pimental](https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/).

Usage

convertCounts(
  counts,
  unit,
  geneLength,
  log = FALSE,
  normalize = "none",
  prior.count = NULL,
  debug = FALSE
)

Arguments

counts	A numeric matrix or dataframe of N genes x M Samples. All columns must be numeric.
unit	Required. One of CPM, FPKM, FPK or TPM.
geneLength	A vector or matrix of gene lengths. Required for length-normalizes units (TPM, FPKM or FPK). If you supply a matrix, the rowMeans are calculated and used.
log	Default = FALSE. Set TRUE to return Log2 values. Employs edgeR functions which use an prior.count of 0.25 scaled by the library size.
normalize	Default = "none". Other options: "TMM", "RLE", "upperquartile" Invokes edgeR::calcNormFactors for normalization. Upperquartile uses the 75th percentile. Normalize settings are case insensitive.
prior.count	Average count to be added to each observation to avoid taking log of zero. Used only if log=TRUE. (Default dependent on method; 0 for TPM, 0.25 for CPM and FPKM) The prior.count is passed to edgeR cpm and rpkm functions and applies to logTPM, logCPM and logFPKM calculations.

Details

geneLength is a vector where length(geneLength) == nrow(counts). If you pass an RSEM effectiveLength matrix, rowMeans(effectiveLength) is used (because edgeR functions only accept a vector for effectiveLength).

Note that log2 values for CPM, TPM and FPKM employ edgeR's prior.count handling to avoid divide by zero.

Value

A matrix in the new unit space

Author(s)

John Thompson, [e-mail]

Examples

#TMM normalized Log2FPKM
Log2FPKM = convertCounts(mycounts),
                      unit="fpkm",
                      geneLength=gene.annotation$ExonLength,
                      log=TRUE,
                      normalize="tmm")

#un-normalized CPM (not logged)
RawCPM = convertCounts(MyCounts,
                      unit="CPM",
                      log=FALSE,
                      normalize="none")

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.