get_features {Rgff}

Analyses the feature type hierarchy of a GFF file

Description

Based on the feature type hierarchy a GFF file, this function creates and returns a feature tree or a feature dependency table.

Usage

get_features(
  inFile,
  includeCounts = FALSE,
  outFormat = c("tree", "data.frame", "JSON"),
  fileType = c("AUTO", "GFF3", "GTF")
)

Arguments

inFile

Path to the input GTF/GFF3 features file

includeCounts

Include number of occurrences of each feature and subfeature

outFormat

Output format of the function. Available formats are: tree (DEFAULT), data.frame and JSON.

fileType

Version of the input file (GTF/GFF3). Default AUTO: determined from the file name.

Value

Depending on the outFormat selected returns a feature tree (tree), a feature dependency table as data.frame (data.frame) or a feature dependency table as JSON object (JSON)

Examples

test_gff3<-system.file("extdata", "AthSmall.gff3", package="Rgff")
get_features(test_gff3)