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#' intersectMatrix
#'
#' This function will count the intersection tally of AVS and genomic regions
#' @param avs A GRanges object which is outputted by loadLd function
#' @param regions A data frame. The data frame contains sample sheet identical to DiffBind or ChIPQC input sample sheets
#' @param ... Heatmap arguments
#' @keywords AVS,Granges
#' @examples
#' \dontrun{
#' intersectMatrix(avs,
#' regions=samples,
#' col=c("white","grey10"),
#' scale="none",
#' margins=c(10,5),
#' cexRow = 1,
#' cexCol = 0.5,
#' Rowv=NA,
#' Colv=NA)
#' }
#' @import GenomicRanges
#' @export
intersectMatrix <- function(avs, regions, ...){
no_of_tags <- length(avs)
no_of_beds <- length(regions$SampleID)
overlap <- matrix(NA, nrow = no_of_beds, ncol = no_of_tags)
for (i in 1:no_of_beds){
bed_path <- as.character(regions$Peaks[i])
bed.gr <- bedToGRanges(bed_path)
overlap[i,] <- ifelse(countOverlaps(avs, bed.gr, ignore.strand=TRUE)>0,1,0)
}
row.names(overlap) <- regions$SampleID
avs.ids <- list()
for (i in 1:length(avs)){
avs.ids <- c(avs.ids, as.character(elementMetadata(avs[[i]])[1,2]))
}
colnames(overlap) <- avs.ids
heatmap(overlap, ...)
return(overlap)
}
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