genomeToTranscript: Map genomic coordinates to transcript coordinates

In ensembldb: Utilities to create and use Ensembl-based annotation databases

Description

genomeToTranscript maps genomic coordinates to positions within the transcript (if at the provided genomic position a transcript is encoded). The function does only support mapping of genomic coordinates that are completely within the genomic region at which an exon is encoded. If the genomic region crosses the exon boundary an empty IRanges is returned. See examples for details.

Usage

genomeToTranscript(x, db)

Arguments

x	GRanges object with the genomic coordinates that should be mapped.
db	EnsDb object.

Details

The function first retrieves all exons overlapping the provided genomic coordinates and identifies then exons that are fully containing the coordinates in x. The transcript-relative coordinates are calculated based on the relative position of the provided genomic coordinates in this exon.

Value

An IRangesList with length equal to length(x). Each element providing the mapping(s) to position within any encoded transcripts at the respective genomic location as an IRanges object. An IRanges with negative start coordinates is returned, if the provided genomic coordinates are not completely within the genomic coordinates of an exon.

The ID of the exon and its rank (index of the exon in the transcript) are provided in the result's IRanges metadata columns as well as the genomic position of x.

Note

The function throws a warning and returns an empty IRanges object if the genomic coordinates can not be mapped to a transcript.

Author(s)

Johannes Rainer

See Also

Other coordinate mapping functions: cdsToTranscript(), genomeToProtein(), proteinToGenome(), proteinToTranscript(), transcriptToCds(), transcriptToGenome(), transcriptToProtein()

Examples

library(EnsDb.Hsapiens.v86)

## Subsetting the EnsDb object to chromosome X only to speed up execution
## time of examples
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X")

## Define a genomic region and calculate within-transcript coordinates
gnm <- GRanges("X:107716399-107716401")

res <- genomeToTranscript(gnm, edbx)
## Result is an IRanges object with the start and end coordinates within
## each transcript that has an exon at the genomic range.
res

## An IRanges with negative coordinates is returned if at the provided
## position no exon is present. Below we use the same coordinates but
## specify that the coordinates are on the forward (+) strand
gnm <- GRanges("X:107716399-107716401:+")
genomeToTranscript(gnm, edbx)

## Next we provide multiple genomic positions.
gnm <- GRanges("X", IRanges(start = c(644635, 107716399, 107716399),
    end = c(644639, 107716401, 107716401)), strand = c("*", "*", "+"))

## The result of the mapping is an IRangesList each element providing the
## within-transcript coordinates for each input region
genomeToTranscript(gnm, edbx)

ensembldb documentation built on Nov. 8, 2020, 4:57 p.m.