Check whether an annotation file contains outlier lines — check_annotation_biomartr • biomartr
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.

# 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.

    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) {
    # 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)
    }