flashfm.input.Rd
Key input for flashfm - constructs snpmod object list and joint effect estimates list for all trait if have external single trait fine-mapping results
flashfm.input(
modPP.list,
beta1.list,
Gmat,
Nall,
ybar.all,
related = FALSE,
y = NULL,
Nsame = NULL,
is.snpmat,
raf = NULL
)
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 probabliity from single trait fine-mapping
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
genotype matrix with SNP columns; could be from sample or reference panel; use unrelated samples
vector of sample sizes; if related samples then give effective sample sizes
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
logical indicating if samples are related (TRUE) or not (FALSE); default is FALSE
(optional) matrix of trait values (trait columns) or indicators of trait measured; used to get joint sample counts; default is NULL and if not provided an approximation is used based on vector of trait sample sizes
(optional) single sample size value, if all traits measured on all individuals
logical taking value TRUE when Gmat is a genotype matrix and FALSE when Gmat is a SNP covariance matrix
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 ans snps in covariance matrix
list containing the main input for flashfm