MGFMwithJAM.RdWrapper for credible sets from Multi-Group Single-Trait Fine-Mapping with JAM
MGFMwithJAM(
gwas.list,
corX.list,
Nall,
save.path,
cpp = 0.99,
cred = 0.99,
maxcv = 1,
maxcv_stop = 20,
NCORES = 1,
jam.nM.iter = 1,
extra.java.arguments = NULL
)List of A data.frame objects, where A is the number of groups; gwas.list[[i]] is a data.frame for group i with 3 columns named: rsID, beta, EAF
List of A data.frame objects, where A is the number of groups; corX.list[[i]] is the SNP correlation matrix for group i
Vector of length A; Nall[i] is the (effective) sample size for group i
Path to save JAM output files; tmp files and could delete these later e.g. save.path=paste0(DIRout,"/tmpJAM/region1").
cumulative posterior probability threshold for selecting top models; default 0.99
Level for credible set, default 0.99
starting value for maximum number of causal variants
maximum value to consider for maximum number of causal variants; maxcv_stop >= maxcv
number of cores for parallel computing; recommend NCORES=A, but if on Windows, use NCORES=1
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 consisting of two objects: CSsummary = List of one data.frame for each trait; each trait data.frame gives the variants in the multi-group credible set for the trait, the mgMPP, pooled MAF, proportion of studies that contain the variant, names of studies that contain the variant CSdetail = [[1]] a list of multi-group credible sets (variants and their mgMPP), one for each trait; [[2]] details = for each trait, list of all multi-group models and variants and their mgPP, mgMPP