FLASHFMZEROwithJAMd.Rd
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
)
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
SNP correlation matrix
Vector of length M; Nall[i] is the (effective) sample size for trait i
Path to save JAM output files; tmp files and could delete these later e.g. save.path=paste0(DIRout,"/tmpJAM/region1").
target odds of no sharing to sharing; default is 1
cumulative posterior probability threshold for selecting top models; default 0.99
number of cores for parallel computing; recommend NCORES=M, but if on Windows, use NCORES=1
starting value for maximum number of causal variants; default 1
maximum value to consider for maximum number of causal variants; maxcv_stop >= maxcv.
in millions, number of iterations to use in JAM; defailt 1 (1 million)
merge groups with minimum between-group r2 > r2.minmerge; default 0.6
only group snps with total MPPI > minsnpmppi; default 0.01
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]])