View source: R/check_annotation.R
check_annotation | R Documentation |
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(annotation_file, remove_annotation_outliers = FALSE)
annotation_file |
a file path tp the annotation file. |
remove_annotation_outliers |
shall outlier lines be removed from the input |
Hajk-Georg Drost
## Not run:
# 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)
## End(Not run)
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