create_testset_multibatch: create_testset_multibatch

In theislab/kBET: k-nearest neighbour batch effect test

create_testset_multibatch

Description

create_testset_multibatch simulates single-cell RNA-seq data as zero-inflated negative binomial counts. The observe several batches that differ from each other - the difference is randomly chosen from the Beta distribution with a = 1, b = 9, i.e. the expected fraction of varied genes is 1/10.

Usage

create_testset_multibatch(n.genes = 1000, n.batch = 3,
  plattform = c("C1", "dropseq", "any"))

Arguments

n.genes	nummber of sampled genes
n.batch	number of batches in the data set
plattform	maximum number of cells (samples) per batch. There are three modes: C1 - 96 cells (max) dropseq - 1000 cells (max) any - 300 cells (max) The number of cell per batch is varied by a Beta distributed random variable to simulate a quality control, where 80% of the samples pass.

Value

list object

1. data - simulated data set with #rows: cells, columns: 'genes'

2. batch - vector with batch identity for each cell

3. comment - 'testSet_multibatch_<n.genes>genes_<n.batch>batches_<plattform>'

Examples

    testdata <- create_testset_multibatch(n.genes=1000, n.batch=3, plattform='any')

theislab/kBET documentation built on Jan. 27, 2024, 9:58 p.m.