fill_in_janno: Fill in a janno table

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

Fill in a janno table

Description

Fill in missing information in a janno table with relevant data from pandora, an eager TSV and the MultiQC general stats table of an eager run using that TSV. Any cells that are already filled in the janno table will be kept as is.

Usage

fill_in_janno(input_janno_table, external_results_table, genotype_ploidy)

Arguments

input_janno_table	A standardised janno tibble, as returned by standardise_janno.
external_results_table	A tibble with the collected results form pandora and eager, as returned by collate_external_results.
genotype_ploidy	character. The genotype ploidy of the genotypes in the dataset. Can be either 'diploid' or 'haploid'.

Value

A tibble with missing values filled in for the fields Collection_ID, Country, Site, Location, Longitude, Latitude, Date_C14_Labnr, Date_BC_AD_Start, Date_BC_AD_Stop, Date_BC_AD_Median, Date_C14_Uncal_BP, Date_C14_Uncal_BP_Err, Date_Type, Nr_Libraries, Capture_Type, UDG, Library_Built, Damage, Nr_SNPs, Endogenous, Contamination, Contamination_Err

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