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

Source: R/flashfm.R

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

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