ABF: Fine-map with ABF

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

Fine-map with ABF

Description

Conduct statistical fine-mapping with Approximate Bayes Factor (ABF) via finemap.abf.

Usage

ABF(
  dat,
  credset_thresh = 0.95,
  compute_n = "ldsc",
  sdY = NULL,
  case_control = TRUE,
  verbose = TRUE
)

Arguments

dat	Fine-mapping results data.
credset_thresh	The minimum mean Posterior Probability (across all fine-mapping methods used) of SNPs to be included in the "mean.CS" column.
compute_n	How to compute per-SNP sample size (new column "N"). If the column "N" is already present in dat, this column will be used to extract per-SNP sample sizes and the argument compute_n will be ignored. If the column "N" is not present in dat, one of the following options can be supplied to compute_n: 0: N will not be computed. >0: If any number >0 is provided, that value will be set as N for every row. **Note**: Computing N this way is incorrect and should be avoided if at all possible. "sum": N will be computed as: cases (N_CAS) + controls (N_CON), so long as both columns are present. "ldsc": N will be computed as effective sample size: Neff =(N_CAS+N_CON)*(N_CAS/(N_CAS+N_CON)) / mean((N_CAS/(N_CAS+N_CON))(N_CAS+N_CON)==max(N_CAS+N_CON)). "giant": N will be computed as effective sample size: Neff = 2 / (1/N_CAS + 1/N_CON). "metal": N will be computed as effective sample size: Neff = 4 / (1/N_CAS + 1/N_CON).
sdY	Standard deviation of quantitative trait.
case_control	Whether the summary statistics come from a case-control study (e.g. a GWAS of having Alzheimer's Disease or not) (TRUE) or a quantitative study (e.g. a GWAS of height, or an eQTL) (FALSE).
verbose	Print messages.

Source

JB Maller et al., Bayesian refinement of association signals for 14 loci in 3 common diseases. Nature Genetics. 44, 1294–1301 (2012).

J Wakefield, A bayesian measure of the probability of false discovery in genetic epidemiology studies. American Journal of Human Genetics. 81, 208–227 (2007).

Examples

dat <- echodata::LRRK2
dat2 <- echofinemap::ABF(dat=dat) 

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