integrate_replicates: integrate_replicates

In shangguandong1996/FindIT2: find influential TF and Target based on multi-omics data

integrate_replicates

Description

integrate value from replicates

Usage

integrate_replicates(
  mt,
  colData,
  fun = NULL,
  type = c("value", "rank", "rank_zscore", "pvalue")
)

Arguments

mt	value matrix
colData	a data.frame with a single column named with "type". Rows of colData correspond to columns of mt.
fun	the function you want to use. If set NULL, program will decide integrate method according to your 'type' parameter.
type	one of 'value', 'rank', 'rank_zscore', pvalue'. value will use mean to integrate replicates, rank will use product, rank_zscore will use Stouffer's method and pvalue will use CCT(Cauchy distribution)

Value

matrix

Examples

mt <- matrix(runif(100, 0, 1), nrow = 10)
colnames(mt) <- paste0(paste0("type", 1:5), "_", rep(1:2, 5))
rownames(mt) <- paste0("TF", 1:10)

colData <- data.frame(
    type = gsub("_[0-9]", "", colnames(mt)),
    row.names = colnames(mt)
)


integrate_replicates(mt, colData, type = "value")

shangguandong1996/FindIT2 documentation built on March 1, 2024, 8:34 p.m.