get_genome_annotation: get_genome_annotation() This function derives GRanges objects...
In BrendelGroup/BWASPR: Various R functions and scripts for the analyis of BWASP workflow output
View source: R/get_genome_annotation.R
get_genome_annotation R Documentation
get_genome_annotation()
This function derives GRanges objects from the GFF3-formatted input file data.
The GFF3 input files should be specified by setup_BWASPR().
Description
get_genome_annotation()
This function derives GRanges objects from the GFF3-formatted input file data.
The GFF3 input files should be specified by setup_BWASPR().
Usage
get_genome_annotation(inputdf)
Arguments
inputdf
A data frame as returned by setup_BWASPR from the input data file.
The data frame contains the directories to specific generic features of DNA and the UTRflag.
Value
A list consisting of GRanges objects that describe generic features of DNA including:
gene,exon,pcexon,promoter,CDS,fpUTR,tpUTR,
fpUTRnotCDS,tpUTRnotCDS,tpUTRunique,ncexon
Examples
mydatf <- system.file("extdata","Am.dat",package="BWASPR")
myparf <- system.file("extdata","Am.par",package="BWASPR")
myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
genome <- get_genome_annotation(myfiles$parameters)
BrendelGroup/BWASPR documentation built on June 2, 2025, 7:25 a.m.
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View source: R/get_genome_annotation.R
| get_genome_annotation | R Documentation |
get_genome_annotation() This function derives GRanges objects from the GFF3-formatted input file data. The GFF3 input files should be specified by setup_BWASPR().
Description
get_genome_annotation() This function derives GRanges objects from the GFF3-formatted input file data. The GFF3 input files should be specified by setup_BWASPR().
Usage
get_genome_annotation(inputdf)
Arguments
inputdf |
A data frame as returned by setup_BWASPR from the input data file. The data frame contains the directories to specific generic features of DNA and the UTRflag. |
Value
A list consisting of GRanges objects that describe generic features of DNA including: gene,exon,pcexon,promoter,CDS,fpUTR,tpUTR, fpUTRnotCDS,tpUTRnotCDS,tpUTRunique,ncexon
Examples
mydatf <- system.file("extdata","Am.dat",package="BWASPR")
myparf <- system.file("extdata","Am.par",package="BWASPR")
myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
genome <- get_genome_annotation(myfiles$parameters)
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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