shiftTranscriptToGenomic {EpiTxDb} | R Documentation

## Shift `GRanges` coordinates based on another `GRanges` object

### Description

`shiftGenomicToTranscript` shifts positions of a `GRanges` object based on coordinates of another `GRanges` object. The most common application is to shift genomic coordinates to transcript coordinates, which is reflected in the name. `shiftTranscriptToGenomic` implements the reverse operation.

Matches are determined by `findOverlaps` for `shiftGenomicToTranscript` and by `findMatches` for `shiftTranscriptToGenomic` using the `seqnames` of the `subject` and the `names` of `tx`.

### Usage

    shiftTranscriptToGenomic(subject, tx)

    shiftGenomicToTranscript(subject, tx)

    ## S4 method for signature 'GRanges,GRangesList'
    shiftTranscriptToGenomic(subject, tx)

    ## S4 method for signature 'GRangesList,GRangesList'
    shiftTranscriptToGenomic(subject, tx)

    ## S4 method for signature 'GRanges,GRangesList'
    shiftGenomicToTranscript(subject, tx)

    ## S4 method for signature 'GRangesList,GRangesList'
    shiftGenomicToTranscript(subject, tx)

### Arguments

`subject` | a `GRanges` or `GRangesList` object
`tx` | a named `GRangesList` object.

### Value

a `GRanges` or `GRangesList` object depending on the type of `subject`

### Examples

    library(GenomicRanges)
    # Construct some example data
    subject1 <- GRanges("chr1", IRanges(3, 6),
                        strand = "+")
    subject2 <- GRanges("chr1", IRanges(c(17,23), width=3),
                        strand = c("+","-"))
    subject3 <- GRanges("chr2", IRanges(c(51, 54), c(53, 59)),
                        strand = "-")
    subject <- GRangesList(a=subject1, b=subject2, c=subject3)
    tx1 <- GRanges("chr1", IRanges(1, 40),
                   strand="+")
    tx2 <- GRanges("chr1", IRanges(10, 30),
                   strand="+")
    tx3 <- GRanges("chr2", IRanges(50, 60),
                   strand="-")
    tx <- GRangesList(a=tx1, b=tx2, c=tx3)

    # shift to transcript coordinates. Since the third subject does not have
    # a match in tx it is dropped with a warning
    shifted_grl <- shiftGenomicToTranscript(subject,tx)

    # ... and back
    shifted_grl2 <- shiftTranscriptToGenomic(shifted_grl,tx)

    # comparison of ranges work. However the seqlevels differ
    ranges(shifted_grl2) == ranges(subject[list(1,c(1,1),c(1,2))])

[Package EpiTxDb version 1.2.1 Index]