prepare.nb.data: Prepare the NB Data Structure for RNA-Seq Read Counts

In NBPSeq: Negative Binomial Models for RNA-Sequencing Data

Prepare the NB Data Structure for RNA-Seq Read Counts

Description

Create a data structure to hold the RNA-Seq read counts and other relevant information.

Usage

prepare.nb.data(counts, lib.sizes = colSums(counts), norm.factors = rep(1,
  dim(counts)[2]), tags = NULL)

Arguments

counts	an mxn matrix of RNA-Seq read counts with rows corresponding to gene features and columns corresponding to independent biological samples.
lib.sizes	an n-vector of observed library sizes. By default, library sizes are estimated to the column totals of the matrix counts.
norm.factors	an n-vector of normalization factors. By default, have values 1 (no normalization is applied).
tags	a matrix of tags associated with genes, one row for each gene (having the same number of rows as counts.

Value

A list containing the following components:

counts	the count matrix, same as input.
lib.sizes	observed library sizes, same as input.
norm.factors	normalization factors, same as input.
eff.lib.sizes	effective library sizes (lib.sizes x norm.factors).
rel.frequencies	relative frequencies (counts divided by the effective library sizes).
tags	a matrix of gene tags, same as input.

NBPSeq documentation built on June 9, 2022, 5:06 p.m.