startRegionString: Get start region as DNA-strings per GRanges group
In ORFik: Open Reading Frames in Genomics
Description
Usage
Arguments
Value
View source: R/feature_helpers.R
Description
One window per start site, if upstream and downstream are both 0, then
only the startsite is returned.
Usage
1
startRegionString(grl, tx, faFile, upstream = 20, downstream = 20)
Arguments
grl
a GRangesList of ranges to find regions in.
tx
a GRangesList of transcripts or (container region),
names of tx must contain all gr names. The names of gr can also be the
ORFik orf names. that is "txName_id".
faFile
FaFile, BSgenome, fasta/index file path or an
ORFik experiment. This file is usually used to find the
transcript sequences from some GRangesList.
upstream
an integer, default (0), relative region to get
upstream from.
downstream
an integer, default (0), relative region to get
downstream from
Value
a character vector of start regions
ORFik documentation built on March 27, 2021, 6 p.m.
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Description Usage Arguments Value
View source: R/feature_helpers.R
Description
One window per start site, if upstream and downstream are both 0, then only the startsite is returned.
Usage
1 | startRegionString(grl, tx, faFile, upstream = 20, downstream = 20)
|
Arguments
grl |
a |
tx |
a |
faFile |
|
upstream |
an integer, default (0), relative region to get upstream from. |
downstream |
an integer, default (0), relative region to get downstream from |
Value
a character vector of start regions
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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