flashfm.Rd
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
)
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.
Vector of target odds of no sharing to sharing
trait covariance matrix
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
cumulative posterior probability threshold for selecting top models; this is ignored when maxmod is spespecified
maximum number of top models to output; NULL by default
logical that is TRUE when fast approximation is used that does not include unequal sample size adjustments; default is FALSE
number of cores for parallel computing; recommend NCORES=M, but if on Windows, use NCORES=1
List consisting of PP: marginal PP for models and MPP: marginal PP of SNP inclusion