SortData: SortData

In SimSeq: Nonparametric Simulation of RNA-Seq Data

Description

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

Usage

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 <[e-mail]>

SimSeq documentation built on May 2, 2019, 5:11 a.m.