R/check_annotation.R
check_annotation.RdSome annotation files include lines with character lengths greater than 65000. This causes problems when trying to import such annotation files into R using import.
To overcome this issue, this function screens for such lines
in a given annotation file and removes these lines so that
import can handle the file.
check_annotation(annotation_file, remove_annotation_outliers = FALSE)a file path tp the annotation file.
shall outlier lines be removed from the input annotation_file?
If yes, then the initial annotation_file will be overwritten and the removed outlier lines will be stored at tempdir
for further exploration.
if (FALSE) {
# download an example annotation file from NCBI RefSeq
Ath_path <- biomartr::getGFF(organism = "Arabidopsis thaliana")
# run annotation file check on the downloaded file
orthologr::check_annotation(Ath_path)
# several outlier lines were detected, thus we re-run the
# function using 'remove_annotation_outliers = TRUE'
# to remove the outliers and overwrite the file
check_annotation(Ath_path, remove_annotation_outliers = TRUE)
}