getGffAttribute {genomeIntervals} | R Documentation |
GFF files contain a string, with key/value pairs separated by “;”, and the key and value separated by “=”. This function quickly extracts one or more key/value pairs.
getGffAttribute(gi, attribute)
gi |
A |
attribute |
A vector of key names. |
A matrix with the same number of rows as gi
, and one column per
element of attribute
.
See parseGffAttributes
for more complete parsing. See the function readGff3
for loading a GFF file.
# Get file path libPath <- installed.packages()["genomeIntervals", "LibPath"] filePath <- file.path( libPath, "genomeIntervals", "example_files" ) # Load gff gff <- readGff3( file.path( filePath, "sgd_simple.gff"), isRightOpen=FALSE) ## head of full gff annotations head(annotation(gff)) # extract ID and Parent attributes idpa = getGffAttribute( gff, c( "ID", "Parent" ) ) head(idpa)