rphast (version 1.0)

tagval.feat: Extract value from tag-value formatted attribute in features object...

Description

Extract value from tag-value formatted attribute in features object

Usage

tagval.feat(x, tag)

Arguments

x

A features object of type feat. The attribute field should be in tag-value format (as described in the GFF 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.

Value

• 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).

Examples

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)