runDiffTPCA {Rtpca} | R Documentation |
Run differential TPCA analysis
runDiffTPCA( objList, contrastList, ctrlCondName = "control", contrastCondName = "treatment", ppiAnno = NULL, complexAnno = NULL, rownameCol = NULL, summaryMethodStr = "median", distMethodStr = "euclidean", n = 10000, p_adj_method = "BH" )
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" |
an object of class tpcaResult with the following slots: 1) ObjList: containing the supplied list of objects
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)