FLASHFMwithJAMd.RdWrapper for flashfm Multi-Trait Fine-Mapping with JAM - this is the dynamic number of max causal variant version
FLASHFMwithJAMd(
gwas.list,
corX,
ybar,
N,
save.path,
TOdds = 1,
covY,
cpp = 0.99,
NCORES,
maxcv = 1,
maxcv_stop = 20,
jam.nM.iter = 1,
extra.java.arguments = NULL
)List of M data.frame objects, where M is the number of traits (at most 6); gwas.list[[i]] is a data.frame for trait i with 3 columns named: rsID, beta, EAF
SNP correlation matrix
trait mean; if trait is transformed to be standard Normal, set ybar = 0, which is default
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
trait covariance matrix (for at most 5 traits and all traits should have a signal in the region, e.g. min p < 1E-6)
cumulative posterior probability threshold for selecting top models; default 0.99
number of cores for parallel computing; recommend NCORES=A, 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)
A character string to be passed through to the java command line. E.g. to specify a different temporary directory by passing "-Djava.io.tmpdir=/Temp".
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]])