Use a set of SNPS, insertions and deletions to modify a reference genome
Usage
genomogrify(x, var, ...)
# S4 method for class 'XStringSet,GRanges'
genomogrify(
x,
var,
alt_col = "ALT",
mask = GRanges(),
tag = NULL,
sep = "_",
var_tags = FALSE,
var_sep = "_",
verbose = TRUE,
...
)
# S4 method for class 'BSgenome,GRanges'
genomogrify(
x,
var,
alt_col = "ALT",
mask = GRanges(),
names,
tag = NULL,
sep = "_",
var_tags = FALSE,
var_sep = "_",
verbose = TRUE,
...
)
# S4 method for class 'BSgenome,VcfFile'
genomogrify(
x,
var,
alt_col = "ALT",
mask = GRanges(),
names,
tag = NULL,
sep = "_",
var_tags = FALSE,
var_sep = "_",
which,
verbose = TRUE,
...
)
# S4 method for class 'XStringSet,VcfFile'
genomogrify(
x,
var,
alt_col = "ALT",
mask = GRanges(),
tag = NULL,
sep = "_",
var_tags = FALSE,
var_sep = "_",
which,
verbose = TRUE,
...
)Arguments
- x
A DNAStringSet or BSgenome
- var
GRanges object containing the variants, or a VariantAnnotation::VcfFile
- ...
Passed to parallel::mclapply
- alt_col
The name of the column with
varcontaining alternate bases- mask
Optional GRanges object defining regions to be masked with an 'N'
- tag
Optional tag to add to all sequence names which were modified
- sep
Separator to place between seqnames names & tag
logical(1) Add tags indicating which type of variant were incorporated, with 's', 'i' and 'd' representing SNPs, Insertions and Deletions respectively
- var_sep
Separator between any previous tags and variant tags
- verbose
logical(1) Print progress messages while running
- names
Sequence names to be mogrified
- which
GRanges object passed to VariantAnnotation::ScanVcfParam if using a VCF directly
Details
This function is designed to create a variant-modified reference genome, intended to be included as a set of decoys when using salmon in selective alignment mode. Sequence lengths will change if InDels are included and any coordinate-based information will be lost on the output of this function.
Tags are able to be added to any modified sequence to assist identifying any changes that have been made to a sequence.
Examples
library(GenomicRanges)
dna <- DNAStringSet(c(chr1 = "ACGT", chr2 = "AATTT"))
var <- GRanges(c("chr1:1", "chr1:3", "chr2:1-3"))
var$ALT <- c("C", "GG", "A")
dna
#> DNAStringSet object of length 2:
#> width seq names
#> [1] 4 ACGT chr1
#> [2] 5 AATTT chr2
genomogrify(dna, var)
#> Updating chr1; Original length: 4
#> ; Updated length: 5
#> Updating chr2; Original length: 5
#> ; Updated length: 3
#> DNAStringSet object of length 2:
#> width seq names
#> [1] 5 CCGGT chr1
#> [2] 3 ATT chr2
genomogrify(dna, var, tag = "mod")
#> Updating chr1; Original length: 4
#> ; Updated length: 5
#> Updating chr2; Original length: 5
#> ; Updated length: 3
#> DNAStringSet object of length 2:
#> width seq names
#> [1] 5 CCGGT chr1_mod
#> [2] 3 ATT chr2_mod
genomogrify(dna, var, var_tags = TRUE)
#> Updating chr1; Original length: 4
#> ; Updated length: 5
#> Updating chr2; Original length: 5
#> ; Updated length: 3
#> DNAStringSet object of length 2:
#> width seq names
#> [1] 5 CCGGT chr1_si
#> [2] 3 ATT chr2_d
genomogrify(dna, var, mask = GRanges("chr2:1-5"), var_tags = TRUE)
#> Applying mask
#> Updating chr1; Original length: 4
#> ; Updated length: 5
#> DNAStringSet object of length 2:
#> width seq names
#> [1] 5 CCGGT chr1_si
#> [2] 5 NNNNN chr2