compile_eager_result_tables: Compile eager results tables

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

Compile eager results tables

Description

Compile together various tables of eager results read into poseidon-compatible tables.

Usage

compile_eager_result_tables(
  tsv_table = NULL,
  sexdet_table = NULL,
  snpcov_table = NULL,
  dmg_table = NULL,
  endogenous_table = NULL,
  nuccont_table = NULL,
  contamination_method = "1",
  contamination_algorithm = "ml",
  XX_cutoffs = c(0.7, 1.2, 0, 0.1),
  XY_cutoffs = c(0.2, 0.6, 0.3, 0.6),
  capture_type = NA_character_
)

Arguments

tsv_table	A tibble with the eager TSV input information as returned by infer_merged_bam_names.
sexdet_table	A tibble with the eager sex determination information as returned by read_sexdet_json.
snpcov_table	A tibble with the eager eigenstrat snp coverage information as returned by read_snp_coverage_json.
dmg_table	A tibble with the eager damageprofiler results, as returned by read_damageprofiler_jsons_from_dir.
endogenous_table	A tibble with the eager endogenous DNA information as returned by read_endorspy_jsons_from_dir.
nuccont_table	A tibble withthe eager nuclear contamination results as returned by read_angsd_cont_json.
contamination_method	The contamination method to keep. Can be either "1" or "2".
contamination_algorithm	The estimation algorithm to keep. Can be "ml" or "mom".
XX_cutoffs	numeric. A vector containing the minimum x_rate, maximum x_rate, minimum y_rate and maximum y_rate for XX calls.
XY_cutoffs	numeric. A vector containing the minimum x_rate, maximum x_rate, minimum y_rate and maximum y_rate for XY calls.
capture_type	character. The Capture_Type. Assumes all libraries have the same one. Defaults to NA, which will disable inference of the Capture_Type and return a dummy column.

Value

A tibble with the compiled information from the provided eager output tables.

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