POLYFUN_run_ldsc: Run a modified version of S-LDSC

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

Run a modified version of S-LDSC

Description

Modifications to S-LDSC include L2-regularization.

Usage

POLYFUN_run_ldsc(
  polyfun = NULL,
  output_dir = NULL,
  munged.path,
  min_INFO = 0.6,
  min_MAF = 0.05,
  annotations.path = file.path(polyfun, "example_data/annotations."),
  weights.path = file.path(polyfun, "example_data/weights."),
  prefix = "LDSC",
  chrom = "all",
  compute_ldscores = FALSE,
  allow_missing_SNPs = TRUE,
  munged_path =
    "/sc/arion/projects/pd-omics/tools/polyfun/Nalls23andMe_2019.sumstats_munged.parquet",
  ref.prefix = "/sc/arion/projects/pd-omics/data/1000_Genomes/Phase1/1000G.mac5eur.",
  freq.prefix = "/sc/arion/projects/pd-omics/tools/polyfun/1000G_frq/1000G.mac5eur.",
  conda_env = "echoR_mini",
  verbose = TRUE
)

Source

https://www.nature.com/articles/s41588-020-00735-5

See Also

Other polyfun: POLYFUN_compute_priors(), 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()

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