getCorMatrix {compartmap} | R Documentation |
This function is used to generate a list object to be passed to getABSignal
getCorMatrix(binmat, squeeze = FALSE)
binmat |
A binned matrix list object from getBinMatrix |
squeeze |
Whether to squeeze the matrix for Fisher's Z transformation |
A list object to pass to getABSignal
library(GenomicRanges) #Generate random genomic intervals of 1-1000 bp on chr1-22 #Modified from https://www.biostars.org/p/225520/ random_genomic_int <- data.frame(chr = rep("chr14", 100)) random_genomic_int$start <- apply(random_genomic_int, 1, function(x) { round(runif(1, 0, getSeqLengths(chr = x)[[1]]), 0) }) random_genomic_int$end <- random_genomic_int$start + runif(1, 1, 1000) random_genomic_int$strand <- "*" #Generate random counts counts <- rnbinom(1000, 1.2, 0.4) #Build random counts for 10 samples count.mat <- matrix(sample(counts, nrow(random_genomic_int) * 10, replace = FALSE), ncol = 10) colnames(count.mat) <- paste0("sample_", seq(1:10)) #Bin counts bin.counts <- getBinMatrix(count.mat, makeGRangesFromDataFrame(random_genomic_int), chr = "chr14", genome = "hg19") #Calculate correlations bin.cor.counts <- getCorMatrix(bin.counts)