POLYFUN_compute_priors: PolyFun: recompute priors

In RajLabMSSM/echofinemap: echoverse module: Fine-mapping functions

PolyFun: recompute priors

Description

Recompute SNP-wise priors from summary stats. Important not on duplicate SNPs: Make sure you have removed all duplicate SNPs from your full summary stats file (fullSS_path) before running this function. Or simply use the remove_dup=TRUE argument. Important note on file formats: Make sure your full summary stats file (fullSS_path) is tab-delimited (NOT space-delimited). This will be done automatically if you set remove_dup=TRUE.

Usage

POLYFUN_compute_priors(
  fullSS_path,
  remove_dup = TRUE,
  polyfun_path = NULL,
  locus_dir = tempdir(),
  sample_size = NULL,
  min_INFO = 0,
  min_MAF = 0.001,
  skip_ckmedian = FALSE,
  num_bins = NULL,
  annotations_path = NULL,
  weights_path = NULL,
  prefix = "dataset1",
  chrom = "all",
  compute_ldscores = FALSE,
  allow_missing_SNPs = TRUE,
  ref_prefix = NULL,
  remove_tmps = TRUE,
  conda_env = "echoR_mini",
  verbose = TRUE
)

Arguments

fullSS_path	Path to the full summary statistics file (GWAS or QTL) that you want to fine-map. It is usually best to provide the absolute path rather than the relative path.
polyfun_path	[Optional] Path to PolyFun directory where all the executables and reference data are stored. Will be automatically installed if set to NULL (default).
locus_dir	Locus-specific directory to store results in.
sample_size	Dataset sample size.
min_INFO	Minimum per-SNP INFO criterion score.
min_MAF	Minimum per-SNP MAF.
skip_ckmedian	SKip ckmedian step.
annotations_path	Path prefix to annotation files #' (e.g. "path/to/files/annotations."). If NULL, will simply use example files included with PolyFun.
weights_path	Path prefix to weights files (e.g. "path/to/files/weights."). If NULL, will simply use example files included with PolyFun.
prefix	Dataset prefix name.
chrom	Which chromosome to query.
compute_ldscores	Whether to compute per-SNP heritability with LDSCore regression.
allow_missing_SNPs	Whether or not to allow missing SNPs.
ref_prefix	Prefix of path leading to reference files.
remove_tmps	Remove temporary files.
conda_env	Conda environment to use.
verbose	Print messages.

See Also

Other polyfun: POLYFUN_download_ref_files(), POLYFUN_find_folder(), POLYFUN_finemapper(), POLYFUN_gather_annotations(), POLYFUN_gather_ldscores(), POLYFUN_help(), POLYFUN_import_priors(), POLYFUN_initialize(), POLYFUN_munge_summ_stats(), POLYFUN_prepare_snp_input(), POLYFUN_run_ldsc(), POLYFUN()

Examples

fullSS_path <- echodata::example_fullSS()
ldsc_files <- echofinemap:::POLYFUN_compute_priors(fullSS_path=fullSS_path)

RajLabMSSM/echofinemap documentation built on Jan. 3, 2023, 1:42 a.m.