get_cdsgrl: Get a set of filtered cds from an imported GTF GRanges
In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities
get_cdsgrl R Documentation
Get a set of filtered cds from an imported GTF GRanges
Description
Get a set of filtered cds from an imported GTF GRanges
Usage
get_cdsgrl(filt_anno, fafileob, ignore_orf_validity)
Arguments
filt_anno
GRanges; an unfilted imported GTF
fafileob
FaFile object; reference to an indexed genomic
fasta file
ignore_orf_validity
Boolean; flag whether to include ORFs
missing a valid stop codon
Details
This takes only coding sequences which are a multiple of 3bp and
have a start and a stop on either end.it always returns coding sequences
without the stops, regardless of their extent in the input.
Value
a GRangesList split by transcript, which contains the filtered coding
ranges for each one
Author(s)
Dermot Harnett, dermot.p.harnett@gmail.com
zslastman/RiboStan documentation built on April 6, 2024, 1:35 p.m.
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| get_cdsgrl | R Documentation |
Get a set of filtered cds from an imported GTF GRanges
Description
Get a set of filtered cds from an imported GTF GRanges
Usage
get_cdsgrl(filt_anno, fafileob, ignore_orf_validity)
Arguments
filt_anno |
GRanges; an unfilted imported GTF |
fafileob |
FaFile object; reference to an indexed genomic fasta file |
ignore_orf_validity |
Boolean; flag whether to include ORFs missing a valid stop codon |
Details
This takes only coding sequences which are a multiple of 3bp and have a start and a stop on either end.it always returns coding sequences without the stops, regardless of their extent in the input.
Value
a GRangesList split by transcript, which contains the filtered coding ranges for each one
Author(s)
Dermot Harnett, dermot.p.harnett@gmail.com
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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