read.gff {gff3Plotter}R Documentation

Reads and Parses GFF3 Data Files of Tiling Array Experiments

Description

Reads and parses GFF3 data files of tiling array experiments to enable further data processing and plotting.

Usage

read.gff(fileName, keepTypes = gffTypes)

Arguments

fileName A single character value for a GFF3 file to load.
keepTypes A vector of strings defining which GFF3 fields should be preserved in the return value: default value is defined by gffTypes <- c("gene", "exon", "insitu", "regulatory_region", "genomic_DNA", "expro")

Details

The return value is split into a list by the TYPE field of GFF3 input file. Values of TYPE that are not in keepTypes are removed. For all elements ATTRIBUTES field will be parced and additional columns will be added (e.g. ID and Name for genes). Finally the ATTRIBUTES field will be removed. Types expro and genomic_DNA are aplit to further lists of experiments based on expName attribute, which is attached as a column to these data. Values START, END, and STRAND of types expro and insitu are updated from corresponding genes.

Value

A list of data.frame-s for basic fields $gene, $exon, $insitu, $genomic_DNA and $expro.

Author(s)

Oleg Sklyar, email:osklyar@ebi.ac.uk

See Also

plot.gff, plot.gff.toFile, getAttr

Examples

   # getting data file name
   dataDir = system.file("extData", package = "gff3Plotter")
   gff3File = paste(dataDir, "test.gff3", sep = "/")

   # running example
   data = read.gff(gff3File)
   xrange = c(100000, 200000)
   subset = gffGetSubset(data, xrange)

[Package gff3Plotter version 1.4.0 Index]