BatchRemove: Batch effect removal

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Batch effect removal

Description

Batch effect removal

Usage

BatchRemove(
  mat,
  batchMat,
  log2trans = FALSE,
  pca = TRUE,
  positive = FALSE,
  cluster = FALSE,
  outdir = NULL
)

Arguments

mat	A data frame, each row is a gene, and each column is a sample.
batchMat	A data frame, the first column should be 'Samples'(matched colnames of mat) and the second column is 'Batch'. The remaining columns could be Covariates.
log2trans	Boolean, specifying whether do logarithmic transformation before batch removal.
pca	Boolean, specifying whether return pca plot.
positive	Boolean, specifying whether all values should be positive.
cluster	Boolean, specifying whether perform hierarchical clustering.
outdir	Output directory for hierarchical cluster tree.

Value

A list contrains two objects, including data and p.

Author(s)

Wubing Zhang

See Also

ComBat

Examples

edata = matrix(c(rnorm(2000, 5), rnorm(2000, 8)), 1000)
colnames(edata) = paste0("s", 1:4)
batchMat = data.frame(sample = colnames(edata), batch = rep(1:2, each = 2))
edata1 = BatchRemove(edata, batchMat)
print(edata1$p)

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.