runDiffTPCA: Run differential TPCA analysis

In nkurzaw/Rtpca: Thermal proximity co-aggregation with R

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)

nkurzaw/Rtpca documentation built on May 12, 2023, 2:10 p.m.