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Check whether an annotation file contains outlier lines

Source: R/check_annotation_biomartr.R
check_annotation_biomartr.Rd

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.

Usage

check_annotation_biomartr(annotation_file, remove_annotation_outliers = FALSE)

Arguments

annotation_file

a file path to the annotation file.

remove_annotation_outliers

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.

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# download an example annotation file from NCBI RefSeq
Ath_path <- biomartr::getGFF(organism = "Arabidopsis thaliana")
# run annotation file check on the downloaded file
biomartr::check_annotation_biomartr(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
biomartr::check_annotation_biomartr(Ath_path, remove_annotation_outliers = TRUE)
} # }