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Build csMR config.yml

csMR_step2_config.yml.Rd

Write an official-style csMR config.yml for Step 3.

Usage

csMR_step2_config.yml(
  repo_dir = "~/Project/software/csMR",
  config.yml_to = "./output/csMR/step2_config/config.yml",
  BASE_OUTPUT_DIR = "./output/csMR/step3_run",
  qtl_input_dir = "./output/csMR/step1_data_preparation/sc_qtl_dir1",
  exposure_ma = "./output/csMR/step1_data_preparation/gwas_exp_p1.ma",
  exposure_id = "exp_p1",
  exposure_type = "cc",
  exposure_ma_dir = NULL,
  outcome_ma_dir = "./output/csMR/step1_data_preparation/outcome",
  GWAS_REFERENCE_GENOTYPE = NULL,
  eQTL_REFERENCE_GENOTYPE = NULL,
  duplicated_snp_path = "None",
  coloc_window_size_bp = 100000L,
  coloc_coverages = 0.9,
  coloc_threads = 5L,
  coloc_cutoff = 0.8
)

Arguments

repo_dir

csMR repository directory.

config.yml_to

Output config file path.

BASE_OUTPUT_DIR

Output root used by csMR Step 3.

qtl_input_dir

Directory of QTL .ma files (or any input supported by .csmr_qtl_paths()).

exposure_ma

Exposure GWAS .ma file path.

exposure_id

Exposure id in GWAS_SUMSTATS.

exposure_type

Exposure type, either "cc" or "quant".

exposure_ma_dir

Optional directory of multiple exposure .ma files. If provided, exposure_ma is ignored and ids are generated from file names.

outcome_ma_dir

Outcome .ma directory (used as OUTCOME_DIR). Must contain only .ma files — Snakemake's os.listdir() picks up every item (incl. .DS_Store, subdirectories) as an outcome wildcard.

GWAS_REFERENCE_GENOTYPE

GWAS reference genotype directory. If NULL, default to repo_dir/data/reference_genome_1000G_EUR.

eQTL_REFERENCE_GENOTYPE

eQTL reference genotype directory. If NULL, default to repo_dir/data/reference_genome_1000G_EUR.

duplicated_snp_path

Path to duplicated SNP file for the reference genotype. Use "None" if not applicable (official csMR default).

coloc_window_size_bp

Coloc window size.

coloc_coverages

Coloc coverage.

coloc_threads

Coloc threads.

coloc_cutoff

Coloc cutoff.

Value

Absolute path to the written config file.

Details

Uppercase arguments such as BASE_OUTPUT_DIR, GWAS_REFERENCE_GENOTYPE, and eQTL_REFERENCE_GENOTYPE intentionally mirror official csMR config.yml keys to keep mapping explicit and reduce confusion when debugging Step 3.

Examples

if (FALSE) { # \dontrun{
out_cfg <- csMR_step2_config.yml(
  repo_dir = "~/Project/software/csMR",
  config.yml_to = "./output/csMR/step2_config/config.yml",
  BASE_OUTPUT_DIR = "./output/csMR/step3_run", # where to store the final csMR output
  qtl_input_dir = "./output/csMR/step1_data_preparation/sc_qtl_dir1",
  exposure_ma = "./output/csMR/step1_data_preparation/gwas_exp_p1.ma",
  exposure_id = "exp_p1",
  exposure_type = "cc",
  outcome_ma_dir = "./output/csMR/step1_data_preparation/outcome"
)
# Example console messages:
# i [23:36:24] Writing csMR config.yml ...
# v [23:36:24] csMR step2 config written: ./output/csMR/step2_config/config.yml
out_cfg
# [1] "/Users/leoarrow/Project/iridocyclitis/output/csMR/step2_config/config.yml"
} # }