multiJAMd.RdWrapper for JAMdynamic single-trait fine-mapping applied to a set of traits, and output SNP groups
multiJAMd(
gwas.list,
corX,
N,
save.path,
maxcv = 1,
maxcv_stop = 20,
jam.nM.iter = 1,
min.mppi = 0.01,
minsnpmppi = 0.01,
r2.minmerge = 0.6,
NCORES = 1,
extra.java.arguments = NULL
)List of M data.frames, where M is the number of traits; gwas.list[[i]] is a data.frame (one for each trait) with 3 columns named: rsID, beta, EAF; if trait names are provided for the M data.frames, these trait names are given in output
SNP correlation matrix that must have snp names in row.names and col.names
scalar that is the trait sample size - same for all traits; if different sample sizes across traits, use flashfm to return single and multi-trait results
Path to save JAM output files; tmp files and could delete these later e.g. save.path=paste0(DIRout,"/tmpJAM/region1").
starting value for maximum number of causal variants
maximum value to consider for maximum number of causal variants; maxcv_stop >= maxcv.
in millions, number of iterations to use in JAM; default 1 (1 million)
trim snp groups with total MPPI < min.mppi in all diseases; default 0.01
only group snps with total MPPI > minsnpmppi; default 0.01
merge groups with minimum between-group r2 > r2.minmerge; default 0.6
number of cores for parallel computing; recommend NCORES=M if running on hpc, but if on Windows/Mac, use NCORES=1
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 consisting of two objects: 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 giving the SNP groups construced under single-trait fine-mapping