import_eager_results: Collect poseidon janno data from an eager TSV and its...

In sidora-tools/eager2poseidon: Automatically fill in Missing Metadata in a Janno File

Collect poseidon janno data from an eager TSV and its corresponding general stats table.

Description

Collect poseidon janno data from an eager TSV and its corresponding general stats table.

Usage

import_eager_results(eager_tsv_fn, general_stats_fn, keep_only, snp_cutoff)

Arguments

eager_tsv_fn	character. Path to the TSV file used as input for the eager run.
general_stats_fn	character. Path to the MultiQC general stats table. Can be found in multiqc/multiqc_data/multiqc_general_stats.txt within the specified eager output directory (--outdir).
keep_only	character. Can be set to "none", "single", or "double". If set to 'single; or 'double', will keep only information for libraries with the specified strandedness. If 'none', all information is retained.
snp_cutoff	integer. The minimum number of SNPs used for nuclear contamination results, for the results to be considered trustworthy. Any values from libraries with fewer than this number of SNPs are ignored.

Value

A tibble containing the poseidon janno fields of Nr_Libraries, Capture_Type, UDG, Library_Built, Damage, Nr_SNPs, Endogenous, Contamination, Contamination_Err, Contamination_Meas, and Contamination_Note

sidora-tools/eager2poseidon documentation built on May 12, 2023, 11:58 p.m.