Prepare the NB Data Structure for RNA-Seq Read Counts

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Description

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

Usage

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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.