MGflashfmRET.RdMulti-group multi-trait fine-mapping, using output from FLASHFMwithJAM or FLASHFMwithFINEMAP; gives both multi- and single-trait results from flashfm object
MGflashfmRET(
gwas.list,
flashfm.list,
Nall,
cred = 0.99,
multi = FALSE,
cpp = 0.99,
NCORES = 1
)List of A lists objects, where A is the number of groups; gwas.list[[i]] is a list for group i with M data.frames (one for each trait) with 3 columns named: rsID, beta, EAF; if trait names are provided for the M data.frames (same names across groups), these trait names are given in output if group names are provided for the A data.frames, these group names are given in the output
List of flashfm output from each of the groups
List of components with same length as number of groups: Nall[[i]] is the M-vector of trait sample sizes for group i, where M is the number of traits
Level for credible set; default 0.99
TRUE for multi-group multi-trait fine-mapping; FALSE for multi-group single-trait fine-mapping; default TRUE
cumulative posterior probability threshold for selecting top models; this is ignored when maxmod is spespecified
number of cores for parallel computing; recommend NCORES=M, but if on Windows, use NCORES=1
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 msMPP, pooled MAF, proportion of groups that contain the variant, names of groups that contain the variant CSdetail = [[1]] a list of multi-group credible sets (variants and their msMPP), one for each trait; [[2]] details = for each trait, list of all multi-group models and variants and their msPP, msMPP