Multi-group multi-trait fine-mapping, using output from FLASHFMwithJAM or FLASHFMwithFINEMAP; gives both multi- and single-trait results from flashfm object

Multi-group multi-trait fine-mapping, using output from FLASHFMwithJAM or FLASHFMwithFINEMAP; gives both multi- and single-trait results from flashfm object

MGflashfm(
  allflashfmPP,
  Nall,
  snps,
  cred = 0.99,
  multi = TRUE,
  cpp = 0.99,
  NCORES = 1
)

Arguments

allflashfmPP

List of components with same length as number of Studies: allflashfmPP[[i]] = flashfmOUT[[i]]$mpp.pp for group i

Nall

List of components with same length as number of Studies: Nall[[i]] is the M-vector of trait sample sizes for group i, where M is the number of traits

snps

vector of all variants that exist in at least one group

cred

Level for credible set; default 0.99

multi

TRUE for multi-group multi-trait fine-mapping; FALSE for multi-group single-trait fine-mapping; default TRUE

cpp

cumulative posterior probability threshold for selecting top models; this is ignored when maxmod is spespecified

NCORES

number of cores for parallel computing; recommend NCORES=M, but if on Windows, use NCORES=1

Value

List consisting of two objects: summary = a list of multi-group credible sets (variants and their msMPP), one for each trait; details = for each trait, list of all multi-group models and variants and their msPP, msMPP

Author

Jenn Asimit