NBPSeq (version 0.1.8)

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

Description

Create a NB 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 = matrix(row.names(counts), dim(counts)[1], 1))

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. By default, row names of the matrix counts are used as tags.

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.