check_annotation_biomartr: Check whether an annotation file contains outlier lines

In biomartr: Genomic Data Retrieval

Check whether an annotation file contains outlier lines

Description

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(s)

Hajk-Georg Drost

Examples

## 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
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)

## End(Not run)

biomartr documentation built on Oct. 25, 2023, 1:08 a.m.