mapToGRanges: Map orfs to genomic coordinates

In Roleren/ORFik: Open Reading Frames in Genomics

Map orfs to genomic coordinates

Description

Creates GRangesList from the results of ORFs_as_List and the GRangesList used to find the ORFs

Usage

mapToGRanges(grl, result, groupByTx = TRUE, grl_is_sorted = FALSE)

Arguments

grl	A GRangesList of the original sequences that gave the orfs in Genomic coordinates. If grl_is_sorted = TRUE (default), negative exon ranges per grl object must be sorted in descending orders.
result	IRangesList A list of the results of finding uorfs list syntax is: Per list group in IRangesList is per grl index. In transcript coordinates. The names are grl index as character.
groupByTx	logical (T), should output GRangesList be grouped by transcripts (T) or by ORFs (F)?
grl_is_sorted	logical, default FALSE If FALSE will sort negative transcript in descending order for you. If you loaded ranges with default methods this is already the case, so you can set to TRUE to save some time.

Details

There is no check on invalid matches, so be carefull if you use this function directly.

Value

A GRangesList of ORFs.

See Also

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

Roleren/ORFik documentation built on Dec. 18, 2024, 11:39 p.m.