pmapToTranscriptF: Faster pmapToTranscript

In JokingHero/ORFik: Open Reading Frames in Genomics

Faster pmapToTranscript

Description

Map range coordinates between features in the transcriptome and genome (reference) space. The length of x must be the same as length of transcripts. Only exception is if x have integer names like (1, 3, 3, 5), so that x[1] maps to 1, x[2] maps to transcript 3 etc.

Usage

pmapToTranscriptF(
  x,
  transcripts,
  ignore.strand = FALSE,
  x.is.sorted = TRUE,
  tx.is.sorted = TRUE
)

Arguments

x	GRangesList/GRanges/IRangesList/IRanges to map to transcriptomic coordinates
transcripts	a GRangesList/GRanges/IRangesList/IRanges to map against (the genomic coordinates). Must be of lower abstraction level than x. So if x is GRanges, transcripts can not be IRanges etc.
ignore.strand	When ignore.strand is TRUE, strand is ignored in overlaps operations (i.e., all strands are considered "+") and the strand in the output is '*'. When ignore.strand is FALSE (default) strand in the output is taken from the transcripts argument. When transcripts is a GRangesList, all inner list elements of a common list element must have the same strand or an error is thrown. Mapped position is computed by counting from the transcription start site (TSS) and is not affected by the value of ignore.strand.
x.is.sorted	if x is a GRangesList object, are "-" strand groups pre-sorted in decreasing order within group, default: TRUE
tx.is.sorted	if transcripts is a GRangesList object, are "-" strand groups pre-sorted in decreasing order within group, default: TRUE

Details

This version tries to fix the shortcommings of GenomicFeature's version. Much faster and uses less memory. Implemented as dynamic program optimized c++ code.

Value

object of same class as input x, names from ranges are kept.

Examples

library(GenomicFeatures)
# Need 2 ranges object, the target region and whole transcript
# x is target region
x <- GRanges("chr1", IRanges(start = c(26, 29), end = c(27, 29)), "+")
names(x) <- rep("tx1_ORF1", length(x))
x <- groupGRangesBy(x)
# tx is the whole region
tx_gr <- GRanges("chr1", IRanges(c(5, 29), c(27, 30)), "+")
names(tx_gr) <- rep("tx1", length(tx_gr))
tx <- groupGRangesBy(tx_gr)
pmapToTranscriptF(x, tx)
pmapToTranscripts(x, tx)

# Reuse names for matching
x <- GRanges("chr1", IRanges(start = c(26, 29, 5), end = c(27, 29, 18)), "+")
names(x) <- c(rep("tx1_1", 2), "tx1_2")
x <- groupGRangesBy(x)
tx1_2 <- GRanges("chr1", IRanges(c(4, 28), c(26, 31)), "+")
names(tx1_2) <- rep("tx1", 2)
tx <- c(tx, groupGRangesBy(tx1_2))

a <- pmapToTranscriptF(x, tx[txNames(x)])
b <- pmapToTranscripts(x, tx[txNames(x)])
identical(a, b)
seqinfo(a)
# A note here, a & b only have 1 seqlength, even though the 2 "tx1"
# are different in size. This is an artifact of using duplicated names.

## Also look at the asTx for a similar useful function.

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.