Reads a GFF or GTF annotation file and returns a dataframe in which the rows correspond to features (e.g. genes or transcripts) and columns correspond to information about the features. Non-ASCII characters are replaced with ASCII equivalents (using the stringi and textclean packages).
Arguments
- file
Character, path to the dataset GFF or GTF file.
- feature_type
Character, the type of feature to extract from the annotation file. Currently supports
'genes'and'transcripts'.- add_fields
Character vector, fields in the GFF/GTF file to extract that are not imported by default (only use if you've run the function once and realised that some fields are not extracted by the function).
Value
A data-frame with the features as rows and features information as columns. Feature IDs are used as row names.
Examples
if (FALSE) { # \dontrun{
import_fmetadata_gff(
"bos_taurus_gene_model.gff3",
"genes",
add_fields = c("name", "description")
)
} # }