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PAINTOR: fine-map

Source: R/PAINTOR.R
PAINTOR.Rd

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_paintor = NULL,
  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
)

Source

GitHub LD Tutorial Input file formats

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_paintor

Character vector of PAINTOR annotation category keywords (e.g., "FANTOM5", "ChromHMM", "DHS", "TFBS"). Set to "all" to use all 10,000+ annotations. Downloads the ~7GB annotation library on first use and caches it.

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.

Examples

if (FALSE) { # \dontrun{
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")
} # }