PAINTOR: PAINTOR: fine-map

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

PAINTOR: fine-map

Description

Run the full PAINTOR fine-mapping pipeline.

Usage

PAINTOR(
  dat,
  LD_matrix,
  locus_dir,
  annot = NULL,
  zscore_col = "ZSCORE",
  tstat_col = "tstat",
  max_causal = 1,
  use_annotations = FALSE,
  annot_xgr = NULL,
  annot_roadmap = NULL,
  chrom_states = NULL,
  credset_thresh = 0.95,
  superpopulation = "EUR",
  LD_reference = "1KGphase3",
  force_new_LD = FALSE,
  method = c("mcmc", "enumerate"),
  seed = 2022,
  paintor_path = NULL,
  force_reinstall = FALSE,
  conda_env = "echoR_mini",
  nThread = 1,
  verbose = TRUE
)

Arguments

dat	Fine-mapping results data.
LD_matrix	Linkage Disequilibrium (LD) matrix to use for fine-mapping.
locus_dir	Locus-specific directory to store results in.
annot	Custom annotations to use for functional fine-mapping.
zscore_col	Name of the column containing the normalized Z-statistic.
tstat_col	[Optional] Name of the column containing the t-statistic.
max_causal	Maximum number of causal SNPs.
use_annotations	Whether to perform functional fine-mapping with specified annotations (TRUE) or simply perform statistical fine-mapping without any annotations.
annot_xgr	Use annotations from XGR via XGR_query.
annot_roadmap	Use annotations from Roadmap via ROADMAP_query.
chrom_states	Filter results by chromatin states.
credset_thresh	The minimum mean Posterior Probability (across all fine-mapping methods used) of SNPs to be included in the "mean.CS" column.
superpopulation	The ancestry of each population in dat. Can be one (applied to all dataset) or more (one per dataset). When users don't supply their own Linkage Disequilibrium (LD) matrix/matrices via the LD_matrix argument, this information is used to gather LD matrices from the reference panel(s) using get_LD.
LD_reference	Name of the LD reference panel.
force_new_LD	Force new LD subset.
method	"enumerate" is actually faster when max_causal is small (<3), but far larger max_causal use "mcmc".
seed	Set the random seed for reproducible results.
paintor_path	[Optional] Path to PAINTOR executable. Will be automatically installed if set to NULL (default).
force_reinstall	Force reinstallation of PAINTOR.
conda_env	Conda environment to use.
nThread	Number of threads to parallelise across (when applicable).
verbose	Print messages.

Source

GitHub LD Tutorial Input file formats

Examples

 
dat <- echodata::BST1
## For example only; 
## normally you need to compute ZSCORE using the 
## full genome-wide summary stats.
dat[,ZSCORE:=(-log10(P))]
LD_matrix <- echodata::BST1_LD_matrix  
locus_dir <- file.path(tempdir(),echodata::locus_dir)
dat2 <- PAINTOR(dat = dat,
                locus_dir = locus_dir,
                LD_matrix = LD_matrix,
                max_causal = 2,
                method = "enumerate") 

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