flashfm: Marginal PP for models of a set of traits, sharing...

In jennasimit/flashfm: flexible and shared information fine-mapping

Marginal PP for models of a set of traits, sharing information between the traits

Description

Marginal PP for models of a set of traits, sharing information between the traits

Usage

flashfm(
  main.input,
  TOdds,
  covY,
  ss.stats,
  cpp = 0.99,
  maxmod = NULL,
  fastapprox = FALSE,
  NCORES
)

Arguments

main.input	List of 3 components: SM=list of snpmod objects for a set of traits; mbeta=list of joint effects for each trait; nsnps= number of SNPs in the region This could be obtained from flashfm.input or JAMexpanded.multi.
TOdds	Vector of target odds of no sharing to sharing
covY	trait covariance matrix
ss.stats	output from summaryStats; list of 4 components: Mx = mean of SNPs, xcovo = covariance matrix of SNPs, Sxy = matrix of Sxy values (column traits), ybar=vector of trait means
cpp	cumulative posterior probability threshold for selecting top models; this is ignored when maxmod is spespecified
maxmod	maximum number of top models to output; NULL by default
fastapprox	logical that is TRUE when fast approximation is used that does not include unequal sample size adjustments; default is FALSE
NCORES	number of cores for parallel computing; recommend NCORES=M, but if on Windows, use NCORES=1

Value

List consisting of PP: marginal PP for models and MPP: marginal PP of SNP inclusion

Author(s)

Jenn Asimit

jennasimit/flashfm documentation built on July 31, 2022, 7:32 p.m.