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Some 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_biomartr(annotation_file, remove_annotation_outliers = FALSE)



a file path to 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.


Hajk-Georg Drost


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
# several outlier lines were detected, thus we re-run the
# function using 'remove_annotation_outliers = TRUE'
# to remove the outliers and overwrite the file
biomartr::check_annotation_biomartr(Ath_path, remove_annotation_outliers = TRUE)