transcriptLocs2refLocs {GenomicFeatures} | R Documentation |
transcriptLocs2refLocs
converts transcript-based
locations into reference-based (aka chromosome-based or genomic)
locations.
transcriptWidths
computes the lengths of the transcripts
(called the "widths" in this context) based on the boundaries
of their exons.
transcriptLocs2refLocs(tlocs, exonStarts=list(), exonEnds=list(), strand=character(0), decreasing.rank.on.minus.strand=FALSE, error.if.out.of.bounds=TRUE) transcriptWidths(exonStarts=list(), exonEnds=list())
tlocs |
A list of integer vectors of the same length as |
exonStarts, exonEnds |
The starts and ends of the exons, respectively. Each argument can be a list of integer vectors,
an IntegerList object,
or a character vector where each element is a
comma-separated list of integers.
In addition, the lists represented by |
strand |
A character vector of the same length as |
decreasing.rank.on.minus.strand |
|
error.if.out.of.bounds |
|
For transcriptLocs2refLocs
: A list of integer vectors of the same
shape as tlocs
.
For transcriptWidths
: An integer vector with one element per
transcript.
Hervé Pagès
extractTranscriptSeqs
for extracting transcript
(or CDS) sequences from chromosomes.
coverageByTranscript
for computing coverage by
transcript (or CDS) of a set of ranges.
## --------------------------------------------------------------------- ## GOING FROM TRANSCRIPT-BASED TO REFERENCE-BASED LOCATIONS ## --------------------------------------------------------------------- library(BSgenome.Hsapiens.UCSC.hg19) # load the genome genome <- BSgenome.Hsapiens.UCSC.hg19 txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite", package="GenomicFeatures") txdb <- loadDb(txdb_file) transcripts <- exonsBy(txdb, by="tx", use.names=TRUE) tx_seqs <- extractTranscriptSeqs(genome, transcripts) ## Get the reference-based locations of the first 4 (5' end) ## and last 4 (3' end) nucleotides in each transcript: tlocs <- lapply(width(tx_seqs), function(w) c(1:4, (w-3):w)) tx_strand <- sapply(strand(transcripts), runValue) ## Note that, because of how we made them, 'tlocs', 'start(exbytx)', ## 'end(exbytx)' and 'tx_strand' have the same length, and, for any ## valid positional index, elements at this position are corresponding ## to each other. This is how transcriptLocs2refLocs() expects them ## to be! rlocs <- transcriptLocs2refLocs(tlocs, start(transcripts), end(transcripts), tx_strand, decreasing.rank.on.minus.strand=TRUE) ## --------------------------------------------------------------------- ## EXTRACTING WORM TRANSCRIPTS ZC101.3 AND F37B1.1 ## --------------------------------------------------------------------- ## Transcript ZC101.3 (is on + strand): ## Exons starts/ends relative to transcript: rstarts1 <- c(1, 488, 654, 996, 1365, 1712, 2163, 2453) rends1 <- c(137, 578, 889, 1277, 1662, 1870, 2410, 2561) ## Exons starts/ends relative to chromosome: starts1 <- 14678410 + rstarts1 ends1 <- 14678410 + rends1 ## Transcript F37B1.1 (is on - strand): ## Exons starts/ends relative to transcript: rstarts2 <- c(1, 325) rends2 <- c(139, 815) ## Exons starts/ends relative to chromosome: starts2 <- 13611188 - rends2 ends2 <- 13611188 - rstarts2 exon_starts <- list(as.integer(starts1), as.integer(starts2)) exon_ends <- list(as.integer(ends1), as.integer(ends2)) transcripts <- IRangesList(start=exon_starts, end=exon_ends) library(BSgenome.Celegans.UCSC.ce2) ## Both transcripts are on chrII: chrII <- Celegans$chrII tx_seqs <- extractTranscriptSeqs(chrII, transcripts, strand=c("+","-")) ## Same as 'width(tx_seqs)': transcriptWidths(exonStarts=exon_starts, exonEnds=exon_ends) transcriptLocs2refLocs(list(c(1:6, 135:140, 1555:1560), c(1:6, 137:142, 625:630)), exonStarts=exon_starts, exonEnds=exon_ends, strand=c("+","-")) ## A sanity check: ref_locs <- transcriptLocs2refLocs(list(1:1560, 1:630), exonStarts=exon_starts, exonEnds=exon_ends, strand=c("+","-")) stopifnot(chrII[ref_locs[[1]]] == tx_seqs[[1]]) stopifnot(complement(chrII)[ref_locs[[2]]] == tx_seqs[[2]])