Reads ninetails read_classes data frame from file.

Imports a single read_classes 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_class_single(class_path, sample_name = NA)

Arguments

class_path

Character string. Path to the ninetails read_classes 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 read_classes 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

After loading, the function applies correct_labels to ensure backward compatibility with the label changes introduced in v0.9 (decorated/blank/unclassified). If the contig column contains GENCODE-formatted identifiers, three additional columns are created: transcript (gene symbol), ensembl_transcript_id_full (with version), and ensembl_transcript_id_short (without version).

Acknowledgements

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

See also

read_class_multiple for batch loading, correct_labels for the backward-compatibility step, check_tails_guppy for the pipeline that produces the input file.

Examples

if (FALSE) { # \dontrun{

class_path <- "/directory/with/ninetails/read_class_output.tsv"
class_data <- ninetails::read_class_single(class_path)

} # }