assignAnnotations: Overlaps GRanges object with provided annotations.
In Roleren/ORFik: Open Reading Frames in Genomics
assignAnnotations R Documentation
Overlaps GRanges object with provided annotations.
Description
It will return same list of GRanges, but with metdata columns:
trainscript_id - id of transcripts that overlap with each ORF
gene_id - id of gene that this transcript belongs to
isoform - for coding protein alignment in relation to cds on coresponding
transcript,
for non-coding transcripts alignment in relation to the transcript.
Usage
assignAnnotations(ORFs, con)
Arguments
ORFs
- GRanges or GRangesList object of your ORFs.
con
- Path to gtf file with annotations.
Value
A GRanges object of your ORFs with metadata columns 'gene',
'transcript', isoform' and 'biotype'.
Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.
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| assignAnnotations | R Documentation |
Overlaps GRanges object with provided annotations.
Description
It will return same list of GRanges, but with metdata columns: trainscript_id - id of transcripts that overlap with each ORF gene_id - id of gene that this transcript belongs to isoform - for coding protein alignment in relation to cds on coresponding transcript, for non-coding transcripts alignment in relation to the transcript.
Usage
assignAnnotations(ORFs, con)
Arguments
ORFs |
- GRanges or GRangesList object of your ORFs. |
con |
- Path to gtf file with annotations. |
Value
A GRanges object of your ORFs with metadata columns 'gene', 'transcript', isoform' and 'biotype'.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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