defineIsoform {ORFik} | R Documentation

## 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.

[Package ORFik version 1.2.1 Index]