read_bedpe: read a BEDPE file into Pairs of GRanges (as if a...

In trichelab/spiky: Spike-in calibration for cell-free MeDIP

read a BEDPE file into Pairs of GRanges (as if a GAlignmentPairs or similar)

Description

read a BEDPE file into Pairs of GRanges (as if a GAlignmentPairs or similar)

Usage

read_bedpe(
  x,
  ...,
  stranded = FALSE,
  fraglen = TRUE,
  optional = FALSE,
  keep = FALSE
)

Arguments

x	a Tabixed BEDPE file, or a TabixFile of one
...	additional arguments to pass to scanTabix internally
stranded	Is the data stranded? (FALSE)
fraglen	compute the fragment length? (TRUE)
optional	scan the optional columns (name, score, strand1)? (FALSE)
keep	keep additional columns? (FALSE)

Details

    BEDPE import in R is a shambles. This is a bandaid on a GSW.
             See the \href{https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format}{BEDPE format definition} for full details.
             In short, for a pair of ranges 1 and 2, we have fields
             chrom1, start1, end1, chrom2, start2, end2, and (optionally)
             name, score, strand1, strand2, plus any other user defined
             fields that may be included (these are not yet supported
             by read_bedpe). For example, two valid BEDPE lines are:

             chr1  100   200   chr5  5000  5100  bedpe_example1  30
             chr9  900  5000   chr9  3000  3800  bedpe_example2  99  +  -

Value

     a Pairs of GRanges, perhaps with $score or $fraglen

See Also

    bedpe_covg

Examples

## Not run: 
  bedpe <- "GSM5067076_2020_A64_bedpe.bed.gz"
  WT1_hg38 <- GRanges("chr11", IRanges(32387775, 32435564), "-")
  read_bedpe(bedpe, param=WT1_hg38)

## End(Not run)

trichelab/spiky documentation built on Sept. 17, 2022, 8:44 a.m.