integrate_replicates {FindIT2} | R Documentation

## 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")

[Package FindIT2 version 1.0.3 Index]