Normalize RNASeq count data using gene lengths

This function normalizes a count matrix, using the matrix of length, and an appropriate transformation.

Usage

lengthNormalizeRNASeq(
  countMatrix,
  lengthMatrix = NULL,
  normalisationFactor = NULL,
  lengthNormalization = c("TPM", "RPKM", "none"),
  dataTransformation = c("log2", "sqrt", "asin(sqrt)")
)

Arguments

countMatrix

The RNASeq count matrix. Rows and columns should be named.

lengthMatrix

The associated length matrix. Should have the same dimensions as countMatrix, with the same names.

normalisationFactor

Normalization factors to scale the raw library sizes, as computed e.g. by calcNormFactors.

lengthNormalization

one of "none" (no correction), "TPM" (default) or "RPKM". See details.

dataTransformation

one of "log2", "asin(sqrt)" or "sqrt." See details.

Value

A matrix of normalized and transformed counts, with the same dimensions as countMatrix.

Details

The normalization procedures are:

none:

No length normalization.

TPM:

TODO

RPKM:

TODO