read.gff {gff3Plotter} | R Documentation |
Reads and parses GFF3 data files of tiling array experiments to enable further data processing and plotting.
read.gff(fileName, keepTypes = gffTypes)
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") |
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.
A list of data.frame
-s for basic fields $gene
, $exon
, $insitu
, $genomic_DNA
and $expro
.
Oleg Sklyar, email:osklyar@ebi.ac.uk
plot.gff
, plot.gff.toFile
, getAttr
# 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)