makeSimCount2groups.filter: Generate count matrix of all null genes

In jhsiao999/ashbun: Methods and evaluation tools for single cell RNA-seq count data

Description

This is an updated version of makeSimCount2groups which takes in filtered data and performs permutation at gene-level and at the sample level.

Usage

makeSimCount2groups.filter(counts, Ngenes = NULL,
  sample_method = c("per_gene", "all_genes"))

Arguments

counts	Gene expression count matrix from a dataset.
Ngenes	Number of genes in the simulated dataset.
Nsample	Number of samples in each condition.
pi0	Proportion of null genes. Default to be 1.

Examples

library(singleCellRNASeqHumanTungiPSC)
eset <- HumanTungiPSC
counts <- exprs(eset)[,pData(eset)$individual == "NA19101"]

sim_counts <- makeSimCount2groups(counts,
                                  Ngenes = 100,
                                  Nsample = 20,
                                  sample_method = "all_genes")

jhsiao999/ashbun documentation built on May 8, 2019, 11:17 p.m.