JAMexpandedCor.multi2 | R Documentation |
Expanded version of JAM (a single-trait fine-mapping approach) that first runs on thinned SNPs and then expands models on tag SNPs; this can run independently on multiple traits This version is more stable than JAMexpandedCor.multi, but slower, so is run only if JAMexpandedCor.multi fails
JAMexpandedCor.multi2(beta1, corX, raf, ybar, Vy, N, r2 = 0.99, save.path)
beta1 |
list where each component is a named vector of of single SNP effect estimates for a trait; one vector for each trait |
corX |
genotype correlation matrix (reference or from sample) |
raf |
named vector of reference allele frequencies; the name of each allele frequency is the SNP ID and MUST be in same SNP order as in corX |
ybar |
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 |
Vy |
vector of trait variances; if related samples, this should be based on unrelated samples; if traits are transformed to be standard Normal, could set Vy as 1-vector |
N |
vector of sample sizes for each trait; recommended to give effective sample sizes using GWAS summary statistics in Neff function |
r2 |
r.squared threshold for thinning SNPs before JAM and finding tag SNPs |
save.path |
path to save JAM output files; tmp files and could delete these later e.g. save.path=paste0(DIRout,"/tmpJAM/region1"). |
list with 3 components: SM a list of snpmod objects giving fine-mapping results for each trait; mbeta a list of joint effect estimates for each trait; nsnps number of SNPs
Jenn Asimit
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.