| SortData {SimSeq} | R Documentation |
SortData
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 <sgbenidt@gmail.com>