uniqueOrder: Get unique ordering for GRangesList groups

In ORFik: Open Reading Frames in Genomics

Description

This function can be used to calculate unique numerical identifiers for each of the GRangesList elements. Elements of GRangesList are unique when the GRanges inside are not duplicated, so ranges differences matter as well as sorting of the ranges.

Usage

uniqueOrder(grl)

Arguments

grl	a GRangesList

Value

an integer vector of indices of unique groups

See Also

uniqueGroups

Other ORFHelpers: defineTrailer(), longestORFs(), mapToGRanges(), orfID(), startCodons(), startSites(), stopCodons(), stopSites(), txNames(), uniqueGroups()

Examples

gr1 <- GRanges("1", IRanges(1,10), "+")
gr2 <- GRanges("1", IRanges(20, 30), "+")
# make a grl with duplicated ORFs (gr1 twice)
grl <- GRangesList(tx1_1 = gr1, tx2_1 = gr2, tx3_1 = gr1)
uniqueOrder(grl) # remember ordering

# example on unique ORFs
uniqueORFs <- uniqueGroups(grl)
# now the orfs are unique, let's map back to original set:
reMappedGrl <- uniqueORFs[uniqueOrder(grl)]

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