## ----style, echo = FALSE, results = 'asis'--------------------------------- BiocStyle::markdown() ## ----lkd, cache=TRUE------------------------------------------------------- suppressPackageStartupMessages(library(ldblock)) path = dir(system.file("hapmap", package="ldblock"), full=TRUE) ceu17 = hmld(path, poptag="CEU", chrom="chr17") ceu17 ## ----abc, fig=TRUE, fig.width=7, fig.height=7------------------------------ library(Matrix) image(ceu17@ldmat[1:400,1:400], col.reg=heat.colors(120), colorkey=TRUE, useRaster=TRUE) ## ----getg------------------------------------------------------------------ library(gwascat) data(ebicat37) seqlevelsStyle(ebicat37) = "NCBI" e17 = ebicat37[ which(as.character(seqnames(ebicat37)) == "17") ] ## ----getrs----------------------------------------------------------------- rsh17 = unique(e17$SNPS) head(rsh17) ## ----doexpa---------------------------------------------------------------- length(rsh17) exset = expandSnpSet( rsh17, ldstruct= ceu17, lb=.9 ) length(exset) all(rsh17 %in% exset)