a list with the following elements

pvalues

P-values for each SNP in dataset 1

N

Number of samples in dataset 1

MAF

minor allele frequency of the variants

beta

regression coefficient for each SNP from dataset 1

varbeta

variance of beta

type

the type of data in dataset 1 - either "quant" or "cc" to denote quantitative or case-control

s

for a case control dataset, the proportion of samples in dataset 1 that are cases

sdY

for a quantitative trait, the population standard deviation of the trait. if not given, it can be estimated from the vectors of varbeta and MAF

snp

a character vector of snp ids, optional. If present, it will be used to merge dataset1 and dataset2. Otherwise, the function assumes dataset1 and dataset2 contain results for the same SNPs in the same order.

Some of these items may be missing, but you must give

• alwaystype

• if type=="cc"s

• if type=="quant" and sdY knownsdY

• if type=="quant" and sdY unknownbeta, varbeta, N, MAF and then either

• pvalues, MAF

• beta, varbeta

as above, for dataset 2

Common minor allele frequency vector to be used for both dataset1 and dataset2, a shorthand for supplying the same vector as parts of both datasets

prior probability a SNP is associated with trait 1, default 1e-4

prior probability a SNP is associated with trait 2, default 1e-4

prior probability a SNP is associated with both traits, default 1e-5