JAMdwithGroups.Rd
Wrapper for JAMdynamic single-trait fine-mapping that also outputs SNP groups; PP and credible sets include SNP group information
JAMdwithGroups(
gwas,
N,
corX,
save.path,
cred = 0.99,
jam.nM.iter = 1,
maxcv = 1,
maxcv_stop = 20,
min.mppi = 0.01,
minsnpmppi = 0.01,
r2.minmerge = 0.6,
extra.java.arguments = NULL
)
data.frame with 3 columns named: rsID, beta, EAF;
scalar that is the trait sample size
SNP correlation matrix that must have snp names in row.names and col.names
Path to save JAM output files; tmp files and could delete these later e.g. save.path=paste0(DIRout,"/tmpJAM/region1").
probability for credible set; default is 0.99
in millions, number of iterations to use in JAM; default 1 (1 million)
starting value for maximum number of causal variants
maximum value to consider for maximum number of causal variants; maxcv_stop >= maxcv.
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 0.5
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 three objects: CS, a data.frame detailing the SNPs in the credible set; 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