Wrapper to run single-trait fine-mapping with JAMexpandedCor.multi on each trait, followed by flashfm and then constuct SNP groups for each approach and summarises results

Wrapper to run single-trait fine-mapping with JAMexpandedCor.multi on each trait, followed by flashfm and then constuct SNP groups for each approach and summarises results

FLASHFMwithJAM(
  beta1,
  corX,
  raf,
  ybar,
  N,
  save.path,
  TOdds = 1,
  covY,
  cpp = 0.99,
  NCORES
)

Arguments

beta1	list where each component is a named vector of of single SNP effect estimates for a trait; one vector for each trait
corX	genotype correlation matrix (reference or from sample)
raf	named vector of reference allele frequencies; the name of each allele frequency is the SNP ID and MUST be in same SNP order as in corX
ybar	vector of trait means; if related samples, this should be based on unrelated samples; if traits are transformed to be standard Normal, could set ybar as 0-vector
N	vector of sample sizes for each trait; recommended to give effective sample sizes using GWAS summary statistics in Neff function
save.path	path to save JAM output files; tmp files and could delete these later e.g. save.path=paste0(DIRout,"/tmpJAM/region1").
TOdds	Vector of target odds of no sharing to sharing
covY	trait covariance matrix (for at most 5 traits and all traits should have a signal in the region, e.g. min p < 1E-6)
cpp	cumulative posterior probability threshold for selecting top models
NCORES	number of cores for parallel computing; recommend NCORES=M, but if on Windows, use NCORES=1

Value

list with 2 components: mpp.pp, a list with 4 components giving the SNP-level results (mpp.pp$PP,mpp.pp$MPP) and SNP group level results (mpp.pp$MPPg, mpp.pp$PPg); and snpGroups, a list with 2 components giving the SNP groups construced under single-trait (snpGroups[[1]]) and multi-trait fine-mapping (snpGroups[[2]])