RNASeqCount.normalize.scale: Normalization of RNA-Seq Reads Count

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Normalization of RNA-Seq Reads Count

Description

RNASeqCount.normalize.scale is a simple version to normalize the RNASeq reads count data.

Usage

RNASeqCount.normalize.scale(mat, total = NULL, pseudoCount = 1)

Arguments

mat	matrix, matrix of RNA-Seq reads data. Each row is a gene/transcript, each column is a sample.
total	integer, total RNA-Seq reads count. If NULL, will use the mean of each column's summation. Default is NULL.
pseudoCount	integer, the integer added to avoid "-Inf" showing up during log transformation. Default is 1.

Details

Users can also load load.exp.RNASeq.demo, and follow the DESeq2 pipeline for RNASeq data processing. Warning, load.exp.RNASeq.demo and load.exp.RNASeq.demoSalmon in NetBID2 may not cover all the possible scenarios.

Value

Return a numeric matrix, containing the normalized RNA-Seq reads count.

Examples

mat1 <- matrix(rnbinom(10000, mu = 10, size = 1),nrow=1000,ncol=10)
colnames(mat1) <- paste0('Sample1',1:ncol(mat1))
rownames(mat1) <- paste0('Gene',1:nrow(mat1))
norm_mat1 <- RNASeqCount.normalize.scale(mat1)

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.