Given the output of fullCoverage, coerce the coverage to a GRanges object.
coerceGR(sample, fullCov, ...)The name or integer index of the sample of interest to coerce
to a GRanges object.
A list where each element is the result from
loadCoverage used with returnCoverage = TRUE. Can be generated
using fullCoverage.
Arguments passed to other methods and/or advanced arguments. Advanced arguments:
If TRUE basic status updates will be printed along
the way.
A named vector with the sequence lengths of the
chromosomes. This argument is passed to GRanges. By
default this is NULL and inferred from the data.
Passed to define_cluster.
A GRanges object with score metadata
vector containing the coverage information for the specified sample. The
ranges reported are only those for regions of the genome with coverage
greater than zero.
## Create a small fullCov object with data only for chr21
fullCov <- list("chr21" = genomeDataRaw)
## Coerce to a GRanges the first sample
gr <- createBwSample("ERR009101",
fullCov = fullCov,
seqlengths = c("chr21" = 48129895)
)
#> 2023-05-07 06:01:10.119523 coerceGR: coercing sample ERR009101
#> 2023-05-07 06:01:10.152385 createBwSample: exporting bw for sample ERR009101
## Explore the output
gr
#> 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
## Coerces fullCoverage() output to GRanges for a given sample