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

FLASHFMwithJAMhat(
  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 6 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]])