R/h5utils.R

In LTLA/diffHic: Differential Analysis of Hi-C Data

.getPairs <- function(y, anchor1, anchor2) { 
	y <- path.expand(y)
	out <- h5read(y, file.path(anchor1, anchor2)) 

    # Eliminating the dimensions from HDF5.
    for (i in seq_along(ncol(out))) {
        out[,i] <- as.vector(out[,i])
    }

    # For legacy purposes:
    colnames(out) <- sub("anchor\\.", "anchor1.", colnames(out))
    colnames(out) <- sub("target\\.", "anchor2.", colnames(out))
    return(out)
}

.initializeH5 <- function(y) {
	y <- path.expand(y)
	if (file.exists(y)) { unlink(y, recursive=TRUE) } 
	if (!h5createFile(y)) { stop(sprintf("failed to create '%s'", y)) }
	return(invisible(NULL))
}

.addGroup <- function(y, anchor) {
	y <- path.expand(y)
	if (!h5createGroup(y, anchor)) { stop("failed to add '%s' group to '%s'", anchor, y) }
	return(invisible(NULL))
}

.writePairs <- function(pairs, y, anchor1, anchor2) {
	y <- path.expand(y)
	rownames(pairs) <- NULL
	if (h5write(pairs, y, file.path(anchor1, anchor2))) { stop("failed to add tag pair data to '%s'", y) }
	return(invisible(NULL))
}

loadChromos <- function(file) 
# A user-accessible function, to see what chromosomes are available in the
# file. This is designed to allow users to pull out one chromosome or another.
#
# written by Aaron Lun
# created 3 November 2014
# last modified 6 January 2016
{
	current <- h5ls(file)
	keep <- current$otype=="H5I_DATASET"
	return(data.frame(anchor1=basename(current$group[keep]), 
            anchor2=current$name[keep], stringsAsFactors=FALSE))
}

loadData <- function(file, anchor1, anchor2) 
# Friendly user-exposed handling of read pair extraction, when the user
# isn't sure of the order of the anchor chromosomes.
#
# written by Aaron Lun
# created 3 November 2014
# last modified 22 November 2015
{
	stopifnot(is.character(anchor1))
	stopifnot(is.character(anchor2))
	stopifnot(is.character(file))
	tryCatch(.getPairs(file, anchor1, anchor2), error=function(e) {
		out <- tryCatch(.getPairs(file, anchor2, anchor1), error=function(e) {
			stop("no dataset corresponding to this anchor combination")
		})
		warning("anchor definitions are reversed")
		out
	})
}