Wrapper for flashfm Multi-Trait Fine-Mapping with JAM (when trait correlation is zero) - this is the dynamic number of max causal variant version

Wrapper for flashfm Multi-Trait Fine-Mapping with JAM (when trait correlation is zero) - this is the dynamic number of max causal variant version

FLASHFMZEROwithJAMd(
  gwas.list,
  corX,
  N,
  save.path,
  TOdds = 1,
  cpp = 0.99,
  NCORES,
  maxcv = 1,
  maxcv_stop = 20,
  jam.nM.iter = 1,
  r2.minmerge = 0.6,
  minsnpmppi = 0.01
)

Arguments

gwas.list

List of M data.frame objects, where M is the number of traits; gwas.list[[i]] is a data.frame for trait i with 3 columns named: rsID, beta, EAF

corX

SNP correlation matrix

N

Vector of length M; Nall[i] is the (effective) sample size for trait i

save.path

Path to save JAM output files; tmp files and could delete these later e.g. save.path=paste0(DIRout,"/tmpJAM/region1").

TOdds

target odds of no sharing to sharing; default is 1

cpp

cumulative posterior probability threshold for selecting top models; default 0.99

NCORES

number of cores for parallel computing; recommend NCORES=M, but if on Windows, use NCORES=1

maxcv

starting value for maximum number of causal variants; default 1

maxcv_stop

maximum value to consider for maximum number of causal variants; maxcv_stop >= maxcv.

jam.nM.iter

in millions, number of iterations to use in JAM; defailt 1 (1 million)

r2.minmerge

merge groups with minimum between-group r2 > r2.minmerge; default 0.6

minsnpmppi

only group snps with total MPPI > minsnpmppi; default 0.01

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 constructed under single-trait (snpGroups[[1]]) and multi-trait fine-mapping (snpGroups[[2]])

Author

Jenn Asimit