make.transformation: Calculates several transformation of counts

In pmoulos/metaseqR: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Description

Returns a list of transformed (normalized) counts, based on the input count matrix data.matrix. The data transformations are passed from the export.scale parameter and the output list is named accordingly. This function is intended mostly for internal use but can also be used independently.

Usage

    make.transformation(data.matrix, export.scale, 
        scf = NULL, log.offset = 1)

Arguments

data.matrix	the raw or normalized counts matrix. Each column represents one input sample.
export.scale	a character vector containing one of the supported data transformations ("natural", "log2", "log10","vst"). See also the main help page of metaseqr.
scf	a scaling factor for the reads of each gene, for example the sum of exon lengths or the gene length. Divided by each read count when export.scale="rpgm". It provides an RPKM-like measure but not the actual RPKM as this normalization is not supported.
log.offset	a number to be added to each element of data.matrix in order to avoid Infinity on log type data transformations.

Value

A named list whose names are the elements in export.scale. Each list member is the respective transformed data matrix.

Author(s)

Panagiotis Moulos

Examples

data.matrix <- round(1000*matrix(runif(400),100,4))
rownames(data.matrix) <- paste("gene_",1:100,sep="")
colnames(data.matrix) <- c("C1","C2","T1","T2")
tr <- make.transformation(data.matrix,c("log2","vst"))
head(tr$vst)

pmoulos/metaseqR documentation built on Dec. 21, 2020, 6:19 a.m.