Key input for flashfm - constructs snpmod object list and joint effect estimates list for all trait if have external single trait fine-mapping results, when trait correlation is zero

Key input for flashfm - constructs snpmod object list and joint effect estimates list for all trait if have external single trait fine-mapping results, when trait correlation is zero

flashfmZero.input(modPP.list, beta1.list, corX, Nall, ybar.all, raf)

Arguments

modPP.list

list of data.frame objects for each trait, containing a column named "snps": snp models of the form "snp1,snp2" and "PP": snp model posterior probability from single trait fine-mapping

beta1.list

list of single SNP effect estimates for each trait in the form of a named vector; name of each effect estimate should appear in Gmat

corX

genotype matrix with SNP columns; could be from sample or reference panel; use unrelated samples

Nall

vector of sample sizes; if related samples then give effective sample sizes

ybar.all

vector of trait means; if related samples, this should be based on unrelated samples; if traits are transformed to be standard Normal, could set ybar as 0-vector

raf

named vector of SNP reference allele frequencies where name is snp id (must match SNP coding used for effect estimates); only needed if Gmat is a covariance matrix and MUST be in same order as SNPs in covariance matrix

Value

list containing the main input for flashfm

Author

Jenn Asimit