get_gff_info: Annotation info
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Details Examples

This function extracts annotation information from a GTF/GFF file.

1	get_gff_info(object=FALSE,gff.file,chr,position,feature=FALSE,extract.gene.names=FALSE)

`object`	object of class `GENOME`
`gff.file`	basepath of the GTF/GFF file
`chr`	the chromosome
`position`	reference positions or region id (when `object` is specified)
`feature`	feature to search for in the gff-file. returns a list of positions
`extract.gene.names`	returns the gene names of the chromosome

This function extracts annotation information from a GTF/GFF file.

1 2	# get_gff_info("Arabidopsis.gff",chr=1,200202) # get_gff_info(GENOME.class,"Arabidopsis.gff",chr=1,position=3)

Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
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querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

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- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

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