Using output from fullCoverage, export the coverage from all the samples to BigWig files using createBwSample.
createBw(fullCov, path = ".", keepGR = TRUE, ...)A list where each element is the result from
loadCoverage used with returnCoverage = TRUE. Can be generated
using fullCoverage.
The path where the BigWig files will be created.
If TRUE, the GRanges objects
created by coerceGR grouped into a GRangesList
are returned. Otherwise they are discarded.
Arguments passed to createBwSample.
If keepGR = TRUE, then a GRangesList
with the output for coerceGR for each of the samples.
Use at most one core per chromosome.
## Create a small fullCov object with data only for chr21
fullCov <- list("chr21" = genomeDataRaw)
## Keep only 2 samples
fullCov$chr21$coverage <- fullCov$chr21$coverage[c(1, 31)]
## Create the BigWig files for all samples in a test dir
dir.create("createBw-example")
bws <- createBw(fullCov, "createBw-example")
#> 2024-12-13 15:13:11.172343 coerceGR: coercing sample ERR009101
#> 2024-12-13 15:13:11.193767 createBwSample: exporting bw for sample ERR009101
#> 2024-12-13 15:13:11.221143 coerceGR: coercing sample SRR031960
#> 2024-12-13 15:13:11.238823 createBwSample: exporting bw for sample SRR031960
#> Warning: There are no bases with coverage > 0 for sample SRR031960. Thus no bw file will be created for this sample.
## Explore the output
bws
#> GRangesList object of length 2:
#> $ERR009101
#> GRanges object with 16 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <integer>
#> chr21 chr21 47410303-47410336 * | 1
#> chr21 chr21 47410687-47410688 * | 1
#> chr21 chr21 47410699-47410734 * | 1
#> chr21 chr21 47410951-47410955 * | 1
#> chr21 chr21 47411924 * | 1
#> ... ... ... ... . ...
#> chr21 chr21 47415237-47415272 * | 1
#> chr21 chr21 47415317-47415352 * | 1
#> chr21 chr21 47417629-47417664 * | 1
#> chr21 chr21 47417674-47417676 * | 1
#> chr21 chr21 47418035-47418067 * | 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome
#>
#> $SRR031960
#> GRanges object with 0 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <integer>
#> -------
#> seqinfo: 1 sequence from an unspecified genome
#>
## First sample
bws[[1]]
#> GRanges object with 16 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <integer>
#> chr21 chr21 47410303-47410336 * | 1
#> chr21 chr21 47410687-47410688 * | 1
#> chr21 chr21 47410699-47410734 * | 1
#> chr21 chr21 47410951-47410955 * | 1
#> chr21 chr21 47411924 * | 1
#> ... ... ... ... . ...
#> chr21 chr21 47415237-47415272 * | 1
#> chr21 chr21 47415317-47415352 * | 1
#> chr21 chr21 47417629-47417664 * | 1
#> chr21 chr21 47417674-47417676 * | 1
#> chr21 chr21 47418035-47418067 * | 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome
## Note that if a sample has no bases with coverage > 0, the GRanges object
## is empty and no BigWig file is created for that sample.
bws[[2]]
#> GRanges object with 0 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <integer>
#> -------
#> seqinfo: 1 sequence from an unspecified genome
## Exports fullCoverage() output to BigWig files