Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../vignettes/ldblock/inst/doc/ldblock.R below:
## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----lkd, cache=TRUE---------------------------------------------------------- suppressPackageStartupMessages({ library(ldblock) library(GenomeInfoDb) }) 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) load(system.file("legacy/ebicat37.rda", package="gwascat")) #seqlevelsStyle(ebicat37) = "NCBI" # noop? seqlevels(ebicat37) = gsub("chr", "", seqlevels(ebicat37)) e17 = ebicat37[ which(as.character(seqnames(ebicat37)) == "17") ] ## ----getrs-------------------------------------------------------------------- rsh17 = unique(e17$SNPS) head(rsh17) ## ----doexpa------------------------------------------------------------------- length(rsh17) exset = ldblock::expandSnpSet( rsh17, ldstruct= ceu17, lb=.9 ) length(exset) all(rsh17 %in% exset)
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