Wrapper for JAMdynamic single-trait fine-mapping that also outputs SNP groups; PP and credible sets include SNP group information

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
)

Arguments

gwas

data.frame with 3 columns named: rsID, beta, EAF;

N

scalar that is the trait sample size

corX

SNP correlation matrix that must have snp names in row.names and col.names

save.path

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

cred

probability for credible set; default is 0.99

jam.nM.iter

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

maxcv

starting value for maximum number of causal variants

maxcv_stop

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

min.mppi

trim snp groups with total MPPI < min.mppi in all diseases; default 0.01

minsnpmppi

only group snps with total MPPI > minsnpmppi; default 0.01

r2.minmerge

merge groups with minimum between-group r2 > r2.minmerge; default 0.5

extra.java.arguments

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".

Value

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

Author

Jenn Asimit