tagval.feat: Extract value from tag-value formatted attribute in features...
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Author(s) Examples

Extract value from tag-value formatted attribute in features object

1	tagval.feat(x, tag)

`x`	A features object of type `feat`. The attribute field should be in tag-value format (either GFF 2 standard; ie, "tag1 val1a val1b; tag2 val2 ; ...", or, GFF 3 standard; ie, "tag1=val1a,val1b;tag2=val2; ...". where vals are in quotes if they are strings.
`tag`	The tag whose values are to be extracted.

If there is at most one relevant value for each feature, a character vector of the same length as x will be returned, containing the value for each feature, or NA where the tag does not exist for that feature. If some elements have multiple values, then the return value will be a list with the same length as x, each element being a character vector containing the values for the corresponding element of x (or NA for no value).

Melissa J. Hubisz

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
featFile <- "sol1.gp"
unzip(exampleArchive, featFile)
f <- read.feat(featFile)
geneName <- tagval.feat(f, "transcript_id")
geneName[1:10]
length(unique(geneName)) # number of unique genes
unlink(featFile)
rm(f, geneName)