Calcluate new exon co-ordinates after including InDels
Arguments
- x
A GenomicRanges object with co-ordinates needing to be recalculated
- var
A set of variants to be incorporated into a reference genome
- alt_col
The name of the column with the alternate sequence for each variant
- mc.cores
Passed internally to
parallel::mclapply()- ...
Not used
Value
GRanges object with co-ordinates shifted according the to the provided
variants. The new co-ordinates will be compatible with a variant-modified
genome as produced by genomogrify() and can be used to extract the
sequences associated with the ranges in the modified reference.
Details
Given a set of variants, this will return a set of genomic ranges with updated co-ordinates able to be applied on a variant modified reference genome
Examples
# Define a 3nt insertion
var <- GRanges("seq1:5:*", seqlengths = c(seq1=10), REF = "A", ALT = "AGT")
var
#> GRanges object with 1 range and 2 metadata columns:
#> seqnames ranges strand | REF ALT
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] seq1 5 * | A AGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome
# A simple GRanges to shift co-ordinates for
gr <- GRanges("seq1:1-10:+", seqlengths = c(seq1=10), feature = "feature1")
gr
#> GRanges object with 1 range and 1 metadata column:
#> seqnames ranges strand | feature
#> <Rle> <IRanges> <Rle> | <character>
#> [1] seq1 1-10 + | feature1
#> -------
#> seqinfo: 1 sequence from an unspecified genome
# Create shifted co-ordinates based on the provided variants
new_gr <- shiftByVar(gr, var)
new_gr
#> GRanges object with 1 range and 1 metadata column:
#> seqnames ranges strand | feature
#> <Rle> <IRanges> <Rle> | <character>
#> [1] seq1 1-12 + | feature1
#> -------
#> seqinfo: 1 sequence from an unspecified genome
## The seqlengths will have been adjusted to account for all variants
seqinfo(new_gr)
#> Seqinfo object with 1 sequence from an unspecified genome:
#> seqnames seqlengths isCircular genome
#> seq1 12 NA <NA>