writeToTallyFile: Writing data to an HDF5 tally file

In h5vc: Managing alignment tallies using a hdf5 backend

Description

This function is used to write the results of a call to tallyRanges to an HDF5 tally file.

Usage

writeToTallyFile( theData, file, study, ranges, samples = NULL )

Arguments

theData	A list of lists of datasets as returned by a call to e.g. tallyRanges
file	The target filename
study	The location of the Group (within the HDF5 file) representing the study the data belongs to.
ranges	A GRanges object defining the ranges that the elements of theData correspond to
samples	The indexes of the samples that the data corresponds to, this can be extracted from the 'Column'-field in the sample metadata and is used to write data corresponding to subsets of the cohort samples. The default (NULL) indicates that all samples are present and will be written.

Author(s)

Paul Theodor Pyl

Examples

suppressPackageStartupMessages(library("h5vc"))
suppressPackageStartupMessages(library("rhdf5"))
files <- list.files( system.file("extdata", package = "h5vcData"), "Pt.*bam$" )
bamFiles <- file.path( system.file("extdata", package = "h5vcData"), files)
suppressPackageStartupMessages(require(BSgenome.Hsapiens.NCBI.GRCh38))
suppressPackageStartupMessages(require(GenomicRanges))
dnmt3a <- read.table(system.file("extdata", "dnmt3a.txt", package = "h5vcData"), header=TRUE, stringsAsFactors = FALSE)
dnmt3a <- with( dnmt3a, GRanges(seqname, ranges = IRanges(start = start, end = end)))
dnmt3a <- reduce(dnmt3a)
require(BiocParallel)
register(MulticoreParam())
theData <- tallyRanges( bamFiles, ranges = dnmt3a[1:3], reference = Hsapiens )
chrom <- "2"
chromlength <- 250e6
study <- "/DNMT3A"
tallyFile <- file.path( tempdir(), "DNMT3A.tally.hfs5" )
if( file.exists(tallyFile) ){
  file.remove(tallyFile)
}
if( prepareTallyFile( tallyFile, study, chrom, chromlength, nsamples = length(files) ) ){
  h5ls(tallyFile)
}else{
  message( paste( "Preparation of:", tallyFile, "failed" ) )
}
writeToTallyFile(theData, tallyFile, study = "/DNMT3A", ranges = dnmt3a[1:3])

h5vc documentation built on Nov. 8, 2020, 4:56 p.m.