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PolyFun: recompute priors

Source: R/POLYFUN_compute_priors.R
POLYFUN_compute_priors.Rd

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.

remove_dup

Whether to remove duplicate SNPs from the full summary stats file before running PolyFun.

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.

num_bins

Number of bins to use for the non-parametric functional enrichment approach. 30 is a reasonable value. If NULL, the default PolyFun behavior is used.

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(), 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()

Examples

if (FALSE) { # \dontrun{
fullSS_path <- echodata::example_fullSS()
ldsc_files <- echofinemap:::POLYFUN_compute_priors(fullSS_path=fullSS_path)
} # }