https://github.com/ChengLiLab/myeloma
Tip revision: 634d6aabda1b3c0bc7ddfe145dfc34b5018b6f63 authored by ChengLiLab on 17 November 2017, 12:16:24 UTC
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Tip revision: 634d6aa
getHicScore.R
# input a pair of translocation sites and Hi-C matrix, get its hi-c interaction score
getHicScore <- function(query, hic_matrix) {
chr1 <- as.integer(strsplit(query[1], split = "chr")[[1]][2])
bin1 <- ceiling( as.numeric(query[2]) / 200000)
chr2 <- as.integer(strsplit(query[5], split = "chr")[[1]][2])
bin2 <- ceiling( as.numeric(query[6]) / 200000)
if ( chr2 < chr1) {
tmp <- chr2
chr2 <- chr1
chr1 <- tmp
tmp <- bin2
bin2 <- bin1
bin1 <- tmp
}
score_1 <- hic_matrix[[chr1]][[chr2]][bin1, bin2]
#score_1 <- hic_matrix[[chr1]][[chr2]][bin1, bin2]
#try(score_2 <- hic_matrix[[chr1]][[chr2]][bin1 +1 , bin2 +1], silent = TRUE)
#if ( !exists("score_2") ) {
# score_2 <- 0
#}
return(c(chr1, chr2, bin1, bin2, score_1))
}