asTX: Map genomic to transcript coordinates by reference

Description Usage Arguments Details Value See Also

View source: R/ranges_helpers.R

Description

Map range coordinates between features in the genome and transcriptome (reference) space.

Usage

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asTX(
  grl,
  reference,
  ignore.strand = FALSE,
  x.is.sorted = TRUE,
  tx.is.sorted = TRUE
)

Arguments

grl

a GRangesList of ranges within the reference, grl must have column called names that gives grouping for result

reference

a GrangesList of ranges that include and are bigger or equal to grl ig. cds is grl and gene can be reference

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

Similar to GenomicFeatures' pmapToTranscripts, but in this version the grl ranges are compared to reference ranges with same name, not by index. And it has a security fix.

Value

a GRangesList in transcript coordinates

See Also

Other ExtendGenomicRanges: coveragePerTiling(), extendLeaders(), extendTrailers(), reduceKeepAttr(), tile1(), txSeqsFromFa(), windowPerGroup()


ORFik documentation built on March 27, 2021, 6 p.m.