scSample {ADAPTS}

Build groupSize pools according to cellIDs

Description

This function is intended to collapse many single cells into 3 (groupsize) groups with the average count across all cells in each of the groups. These groups can then be used to perform a t-test (for example) between the 3 groups of CellX with 3 groups of CellY

Usage

scSample(
  RNAcounts,
  cellIDs = colnames(RNAcounts),
  groupSize = 3,
  randomize = TRUE,
  mc.cores = 1
)

Arguments

RNAcounts

The single cell matrix

cellIDs

A vector will cell types for each column in scCountMatrix (DEFAULT: colnames(RNAcounts))

groupSize

The number of sets to break it up into (DEFAULT: 3)

randomize

Set to TRUE to randomize the sets (DEFAULT: TRUE)

mc.cores

The number of cores to use (DEFAULT: 1)

Value

a list with a multiple sets

Examples

RNAcounts <- matrix(0, nrow=10, ncol=100)
rownames(RNAcounts) <- make.names(rep('Gene', nrow(RNAcounts)), unique=TRUE)
colnames(RNAcounts) <- make.names(c('CellX', rep('CellY', 39), 
rep('CellZ', 30), rep('CellB', 30)), unique=TRUE)
RNAcounts[, grepl('CellY', colnames(RNAcounts))] <- 1
RNAcounts[, grepl('CellZ', colnames(RNAcounts))] <- 2
RNAcounts[, grepl('CellB', colnames(RNAcounts))] <- 3
scSample(RNAcounts, groupSize=3)