Make table of fine-mapping results output from "flashfm" (flashfmZero or flashfm), "multiJAMd", or "JAMdwithGroups"

Make table of fine-mapping results output from "flashfm" (flashfmZero or flashfm), "multiJAMd", or "JAMdwithGroups"

FMsummary_table(FMout, method = "flashfm", traitnames = NULL, cred = 0.99)

Arguments

FMout

object output from "flashfm" (flashfmZero or flashfm related wrappers, like "FLASHFMZEROwithJAMd"), "multiJAMd", or "JAMdwithGroups"

method

text for fine-mapping method used, i.e. one of "flashfm" (flashfmZero or flashfm), "multiJAMd", or "JAMdwithGroups"

traitnames

vector of trait names (same length as number of traits that were fine-mapped) and in same order as fine-mapped traits

cred

level used for credible set construction; default is 0.99

Value

Table where each row corresponds to one trait, listing credible set size, details of variant with maximum MPP, variants with MPP>0.90 and snp groups coinciding with the variant(s)

Author

Jenn Asimit