Shift GRanges coordinates based on another GRanges object

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.

shiftTranscriptToGenomic(subject, tx)

shiftGenomicToTranscript(subject, tx)

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

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

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

# S4 method for class '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)
#> Warning: Dropping elements of 'subject' which could not be repositioned.

# ... 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))])
#> Warning: longer argument not a multiple of length of shorter
#> LogicalList of length 4
#> [["a"]] TRUE
#> [["a"]] FALSE FALSE
#> [["b"]] FALSE FALSE
#> [["c"]] FALSE FALSE