defineIsoform: Overlaps GRanges object with provided annotations.

In JokingHero/ORFik: Open Reading Frames in Genomics

Overlaps GRanges object with provided annotations.

Description

Overlaps GRanges object with provided annotations.

Usage

defineIsoform(
  rel_orf,
  tran,
  isoform_names = c("perfect_match", "elong_START_match", "trunc_START_match",
    "elong_STOP_match", "trunc_STOP_match", "overlap_inside", "overlap_both",
    "overlap_upstream", "overlap_downstream", "upstream", "downstram", "none")
)

Arguments

rel_orf	- GRanges object of your ORF.
tran	- GRanges object of annotation (transcript or cds) that overlapped in some way rel_orf.
isoform_names	- A vector of strings that will be used instead of these defaults: 'perfect_match' - start and stop matches the tran object strand wise 'elong_START_match' - rel_orf is extension from the STOP side of the tran 'trunc_START_match' - rel_orf is truncation from the STOP side of the tran 'elong_STOP_match' - rel_orf is extension from the START side of the tran 'trunc_STOP_match' - rel_orf is truncation from the START side of the tran 'overlap_inside' - rel_orf is inside tran object 'overlap_both' - rel_orf contains tran object inside 'overlap_upstream' - rel_orf is overlaping upstream part of the tran 'overlap_downstream' - rel_orf is overlaping downstream part of the tran 'upstream' - rel_orf is upstream towards the tran 'downstream' - rel_orf is downstream towards the tran 'none' - when none of the above options is true

Value

A string object of defined isoform towards transcript.

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.