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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/transcriptLocs2refLocs.R

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

1
2
3
4
5
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.

Author(s)

Hervé Pagès

See Also

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
## ---------------------------------------------------------------------
## WITH A SMALL SET OF HUMAN TRANSCRIPTS
## ---------------------------------------------------------------------
txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                         package="GenomicFeatures")
txdb <- loadDb(txdb_file)
ex_by_tx <- exonsBy(txdb, by="tx", use.names=TRUE)
genome <- BSgenome::getBSgenome("hg19")  # load the hg19 genome
tx_seqs <- extractTranscriptSeqs(genome, ex_by_tx)

## 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(ex_by_tx), runValue)

## Note that, because of how we made them, 'tlocs', 'start(ex_by_tx)',
## 'end(ex_by_tx)' and 'tx_strand' are "parallel" objects i.e. they
## 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(ex_by_tx), end(ex_by_tx),
             tx_strand, decreasing.rank.on.minus.strand=TRUE)

## ---------------------------------------------------------------------
## WITH TWO WORM TRANSCRIPTS: ZC101.3.1 AND F37B1.1.1
## ---------------------------------------------------------------------
library(TxDb.Celegans.UCSC.ce11.ensGene)
txdb <- TxDb.Celegans.UCSC.ce11.ensGene
my_tx_names <- c("ZC101.3.1", "F37B1.1.1")
## Both transcripts are on chromosome II, the first one on its positive
## strand and the second one on its negative strand:
my_tx <- transcripts(txdb, filter=list(tx_name=my_tx_names))
my_tx

## Using transcripts stored in a GRangesList object:
ex_by_tx <- exonsBy(txdb, use.names=TRUE)[my_tx_names]
genome <- getBSgenome("ce11")  # load the ce11 genome
tx_seqs <- extractTranscriptSeqs(genome, ex_by_tx)
tx_seqs

## Since the 2 transcripts are on the same chromosome, an alternative
## is to store them in an IRangesList object and use that object with
## extractTranscriptSeqs():
ex_by_tx2 <- ranges(ex_by_tx)
tx_seqs2 <- extractTranscriptSeqs(genome$chrII, ex_by_tx2,
                                  strand=strand(my_tx))
stopifnot(identical(as.character(tx_seqs), as.character(tx_seqs2)))

## Store exon starts and ends in two IntegerList objects for use with
## transcriptWidths() and transcriptLocs2refLocs():
exon_starts <- start(ex_by_tx)
exon_ends <- end(ex_by_tx)

## Same as 'width(tx_seqs)':
transcriptWidths(exonStarts=exon_starts, exonEnds=exon_ends)

transcriptLocs2refLocs(list(c(1:2, 202:205, 1687:1688),
                            c(1:2, 193:196, 721:722)),
                       exonStarts=exon_starts,
                       exonEnds=exon_ends,
                       strand=c("+","-"))

## A sanity check:
ref_locs <- transcriptLocs2refLocs(list(1:1688, 1:722),
                                   exonStarts=exon_starts,
                                   exonEnds=exon_ends,
                                   strand=c("+","-"))
stopifnot(genome$chrII[ref_locs[[1]]] == tx_seqs[[1]])
stopifnot(complement(genome$chrII)[ref_locs[[2]]] == tx_seqs[[2]])

Bioconductor/GenomicFeatures documentation built on May 25, 2021, 5:47 a.m.