Proteins object containing peptides
pranges to be mapped.
A GRangesList object used to map
between x and the result. The ranges are typically created by
the etrid2grl function.
TRUE (default) or FALSE. Should
empty ranges be dropped?
Additional parameters passed to inner
functions. Currently ignored.
mapToGenome maps the pranges(x) to the ranges of
genome. Unless x and genome are of length 1,
both must be named and items of x are matched to items of
genome using their respective names. Names that do not
co-occur in x and genome are ignored. If we have
seqnames(x): "A", "B" and "C"
names(genome): "C", "A", "a",
"z", "A" and "A".
the names of the output will be
"A", "A", "A" and "C".
The output is ordered by (1) seqnames(x) and (2) the order of
the elements in genome.
In case less than length(x) are mapped, as for p["B"]
above, a message informs the user.
pmapToGenome is the element-wise (aka 'parallel')
version of mapToGenome. The i-th pranges(x) is mapped
to the i-th range in genome. x and genome must
have the same length and do not need to be named (names are
A named GRangesList object, with names matching
names(genome). For pmapToGenome, the return value will
have the same length as the inputs.
See ?mapToAlignments in the
GenomicAlignments package for mapping coordinates between
reads (local) and genome (reference) space using a CIGAR
See ?mapToTranscripts in the
GenomicRanges package for mapping coordinates between features
in the transcriptome and genome space.
The proteinCoding function to remove non-protein
coding ranges before mapping peptides to their genomic coordinates.
The mapping vignette for examples and visualisations.
See plotAsAnnotationTrack and
plotAsAnnotationTrack for more details about the two