Use a set of SNPs, insertions and deletions to modify a reference transcriptome
Usage
transmogrify(x, var, exons, ...)
# S4 method for class 'XStringSet,GRanges,GRanges'
transmogrify(
x,
var,
exons,
alt_col = "ALT",
trans_col = "transcript_id",
omit_ranges = NULL,
tag = NULL,
sep = "_",
var_tags = FALSE,
var_sep = "_",
verbose = TRUE,
mc.cores = 1,
...
)
# S4 method for class 'BSgenome,GRanges,GRanges'
transmogrify(
x,
var,
exons,
alt_col = "ALT",
trans_col = "transcript_id",
omit_ranges = NULL,
tag = NULL,
sep = "_",
var_tags = FALSE,
var_sep = "_",
verbose = TRUE,
mc.cores = 1,
...
)
# S4 method for class 'BSgenome,VcfFile,GRanges'
transmogrify(
x,
var,
exons,
alt_col = "ALT",
trans_col = "transcript_id",
omit_ranges = NULL,
tag = NULL,
sep = "_",
var_tags = FALSE,
var_sep = "_",
verbose = TRUE,
mc.cores = 1,
which,
...
)
# S4 method for class 'XStringSet,VcfFile,GRanges'
transmogrify(
x,
var,
exons,
alt_col = "ALT",
trans_col = "transcript_id",
omit_ranges = NULL,
tag = NULL,
sep = "_",
var_tags = FALSE,
var_sep = "_",
verbose = TRUE,
mc.cores = 1,
which,
...
)Arguments
- x
Reference genome as either a DNAStringSet or BSgenome
- var
GRanges object containing the variants
- exons
GRanges object with ranges representing exons
- ...
Passed to parallel::mclapply
- alt_col
Column from
varcontaining alternate bases- trans_col
Column from 'exons' containing the transcript_id
- omit_ranges
GRanges object containing ranges to omit, such as PAR-Y regions, for example
- 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) Include informative messages, or operate silently
- mc.cores
Number of cores to be used when multi-threading via parallel::mclapply
- which
GRanges object passed to VariantAnnotation::ScanVcfParam if using a VCF directly
Details
Produce a set of variant modified transcript sequences from a standard reference genome. Supported variants are SNPs, Insertions and Deletions
Ranges needing to be masked, such as the Y-chromosome, or Y-PAR can be provided.
It should be noted that this is a time consuming process Inclusion of a large set of insertions and deletions across an entire transcriptome can involve individually modifying many thousands of transcripts, which can be a computationally demanding task. Whilst this can be parallelised using an appropriate number of cores, this may also prove taxing for lower power laptops, and pre-emptively closing memory hungry programs such as Slack, or internet browers may be prudent.
Examples
library(GenomicRanges)
library(GenomicFeatures)
seq <- DNAStringSet(c(chr1 = "ACGTAAATGG"))
exons <- GRanges(c("chr1:1-3:-", "chr1:7-9:-"))
exons$transcript_id <- c("trans1")
# When using extractTranscriptSeqs -stranded exons need to be sorted by end
exons <- sort(exons, decreasing = TRUE, by = ~end)
exons
#> GRanges object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | transcript_id
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 7-9 - | trans1
#> [2] chr1 1-3 - | trans1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
trByExon <- splitAsList(exons, exons$transcript_id)
# Check the sequences
seq
#> DNAStringSet object of length 1:
#> width seq names
#> [1] 10 ACGTAAATGG chr1
extractTranscriptSeqs(seq, trByExon)
#> DNAStringSet object of length 1:
#> width seq names
#> [1] 6 CATCGT trans1
# Define some variants
var <- GRanges(c("chr1:2", "chr1:8"))
var$ALT <- c("A", "GGG")
# Include the variants adding tags to indicate a SNP and indel
# The exons GRanges object will be split by transcript internally
transmogrify(seq, var, exons, var_tags = TRUE)
#> 1 transcripts found with indels
#> DNAStringSet object of length 1:
#> width seq names
#> [1] 8 CCCCTCTT trans1_si