SortData

Share:

Description

A function called in SimData used to trim and sort the matrix of counts provided.

Usage

1
SortData(counts, treatment, replic = NULL, sort.method, norm.factors = NULL)

Arguments

counts

A matrix of counts where each row specifies a gene and each column specifies a replicate.

treatment

A vector specifying the treatment group for each column of the counts matrix. Only two treatment groups of either paired or unpaired data are allowed.

replic

A vector specifying the replicate for each column of the counts matrix when there is paired data; optional if data is unpaired.

sort.method

Character vector specifying one of "unpaired" or "paired", depending on the structure of the data.

norm.factors

An optional positive numeric vector of multiplicative normalization factors for each column of the counts matrix.

Value

List containing:

counts

sorted and trimmed matrix of counts.

replic

sorted and trimmed replic vector.

treatment

sorted and trimmed treatment vector.

norm.factors

sorted and trimmed offset vector.

sorting

sorting vector used to sort and trim.

Author(s)

Samuel Benidt <sgbenidt@gmail.com>