Reads ninetails nonadenosine_residues data from file.

Imports a single nonadenosine_residues output file produced by check_tails_guppy (or other ninetails pipelines) into R. Optionally attaches a sample identifier and parses GENCODE-style contig names into Ensembl transcript IDs.

Usage

read_residue_single(residue_path, sample_name = NA)

Arguments

residue_path

Character string. Path to the ninetails nonadenosine_residues output file (.tsv).

sample_name

Character string (optional, default NA). If specified, added as a factor column sample_name. Overwrites any existing sample_name column with a warning.

Value

A tibble containing non-A residue predictions with the following additional columns (when GENCODE contigs are present):

transcript

Character. Gene symbol parsed from GENCODE contig.

ensembl_transcript_id_full

Character. Ensembl transcript ID with version number.

ensembl_transcript_id_short

Character. Ensembl transcript ID without version number.

Details

If the contig column contains GENCODE-formatted identifiers, three additional columns are created: transcript, ensembl_transcript_id_full, and ensembl_transcript_id_short (see read_class_single for the same logic applied to class data).

Acknowledgements

Function based on read_polya_single from the NanoTail package by P. Krawczyk (smaegol): https://github.com/LRB-IIMCB/nanotail/.

See also

read_residue_multiple for batch loading, read_class_single for the analogous class data loader, check_tails_guppy for the pipeline that produces the input file.

Examples

if (FALSE) { # \dontrun{

residue_path <- "/directory/with/ninetails/nonadenosine_residues_output.tsv"
residue_data <- ninetails::read_residue_single(residue_path)

} # }