GenomicFeatures (version 1.24.4)

transcriptLocs2refLocs: Converting transcript-based locations into reference-based locations

Description

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.

Usage

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())

Arguments

tlocs

A list of integer vectors of the same length as exonStarts and exonEnds. Each element in tlocs must contain transcript-based locations.

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 exonStarts and exonEnds must have the same shape i.e. have the same lengths and have elements of the same lengths. The length of exonStarts and exonEnds is the number of transcripts.

strand

A character vector of the same length as exonStarts and exonEnds specifying the strand ("+" or "-") from which the transcript is coming.

decreasing.rank.on.minus.strand

TRUE or FALSE. Describes the order of exons in transcripts located on the minus strand: are they ordered by increasing (default) or decreasing rank?

error.if.out.of.bounds

TRUE or FALSE. Controls how out of bound tlocs are handled: an error is thrown (default) or NA is returned.

Value

For transcriptLocs2refLocs: A list of integer vectors of the same shape as tlocs.For transcriptWidths: An integer vector with one element per transcript.

See Also

• extractTranscriptSeqs for extracting transcript (or CDS) sequences from chromosomes.

• coverageByTranscript for computing coverage by transcript (or CDS) of a set of ranges.

Examples

## ---------------------------------------------------------------------
## 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]])