runDiffTPCA {Rtpca} | R Documentation

## Run differential TPCA analysis

### Description

Run differential TPCA analysis

### Usage

    runDiffTPCA(
      objList,
      contrastList,
      ctrlCondName = "control",
      contrastCondName = "treatment",
      ppiAnno = NULL,
      complexAnno = NULL,
      rownameCol = NULL,
      summaryMethodStr = "median",
      distMethodStr = "euclidean",
      n = 10000,
      p_adj_method = "BH"
    )

### Arguments

`objList` | input list of objects, e.g. ExpressionSets retrieved after TPP data import or matrices or data frames
`contrastList` | input list of objects for comparison at e.g. different treatment condtion, same file formats work as for objList
`ctrlCondName` | character string indicating the name of the control condition, default is "control"
`contrastCondName` | character string indicating the name of the contrast condition, default is "treatment"
`ppiAnno` | data frame annotation known protein-protein interactions (PPI) to test
`complexAnno` | data frame annotating known protein complexes of interest to test
`rownameCol` | in case the input objects are tibbles this parameter takes in the name (character) of the column specifying protein names or ids
`summaryMethodStr` | character string indicating a method to use to summarize measurements across replicates, default is "median", other options are c("mean", "rbind")
`distMethodStr` | method to use within dist function, default is 'euclidean'
`n` | number of random protein pair draws to obtain empirical p-value, default is 10000
`p_adj_method` | method to be used for multiple testing adjusment, default is "BH"

### Value

an object of class tpcaResult with the following slots: 1) ObjList: containing the supplied list of objects

### Examples

    library(dplyr)
    library(Biobase)

    m1 <- matrix(1:28, ncol = 4)
    m2 <- matrix(2:25, ncol = 4)
    m3 <- matrix(c(2:10, 1:19), ncol = 4)

    rownames(m1) <- 1:7
    rownames(m2) <- 3:8
    rownames(m3) <- 2:8

    mat_list <- list(
        m1, m2, m3
    )

    c1 <- matrix(29:2, ncol = 4)
    c2 <- matrix(26:3, ncol = 4)
    c3 <- matrix(c(11:3, 20:2), ncol = 4)

    rownames(c1) <- 1:7
    rownames(c2) <- 3:8
    rownames(c3) <- 2:8

    contrast_list <- list(
        c1, c2, c3
    )

    ppi_anno <- tibble(
        x = c("3", "3"),
        y = c("5", "7"),
        pair = c("3:5", "3:7"))

    ref_df <- tibble(
        pair = c("3:5", "3:7"),
        valueC2 = c(4, 8)
    )

    diff_tpca <- Rtpca:::runDiffTPCA(
      mat_list, contrast_list, ppiAnno = ppi_anno)

[Package Rtpca version 1.2.0 Index]