## ----setup, include=FALSE, cache=FALSE---------------------------------------- knitr::opts_chunk$set(echo = TRUE) #knitr::opts_knit$set(root.dir="") ## ----installation, echo=TRUE, eval=FALSE-------------------------------------- # if(!requireNamespace("BiocManager")){ # install.packages("BiocManager") # } # if(!requireNamespace("MAGAR")){ # BiocManager::install("MAGAR") # } ## ----loading, eval=TRUE------------------------------------------------------- suppressPackageStartupMessages(library(MAGAR)) ## ----options, eval=TRUE------------------------------------------------------- opts <- rnb.xml2options(system.file("extdata","rnbeads_options.xml",package="MAGAR")) rnb.options(identifiers.column="geo_accession", import.idat.platform="probes450") xml.fi <- file.path(getwd(),"rnbeads_options.xml") cat(rnb.options2xml(),file=xml.fi) qtlSetOption(rnbeads.options = xml.fi) ## ----plink_folder, eval=FALSE------------------------------------------------- # geno.dir <- "plink_data" # rnb.set <- load.rnb.set("rnb_set_dir") # s.anno <- "sample_annotation.csv" # data.loc <- list(idat.dir=rnb.set,geno.dir=plink.dir) # qtlSetOption(geno.data.type="plink", # meth.data.type="rnb.set") # meth.qtl <- doImport(data.location=data.loc, # s.anno=s.anno, # s.id.col="SampleID", # out.folder=getwd()) ## ----imputation options, eval=TRUE-------------------------------------------- qtlSetOption( impute.geno.data=TRUE, imputation.reference.panel="apps@hrc-r1.1", imputation.phasing.method="shapeit", imputation.population="eur" ) ## ----imputed_import,eval=FALSE------------------------------------------------ # idat.dir <- "idat_dir" # geno.dir <- "geno_dir" # anno.sheet <- "sample_annotation.tsv" # qtlSetOption(hdf5dump=TRUE) # imp.data <- doImport(data.location = c(idat.dir=idat.dir,geno.dir=geno.dir), # s.anno = anno.sheet, # s.id.col = "ID", # tab.sep = "\t", # out.folder = getwd()) ## ----call_methQTL, eval=TRUE-------------------------------------------------- imp.data <- loadMethQTLInput(system.file("extdata","reduced_methQTL",package="MAGAR")) qtlSetOption(standard.deviation.gauss=100, cluster.cor.threshold=0.75) meth.qtl.res <- doMethQTL(imp.data,default.options=FALSE,p.val.cutoff=0.05) ## ----show_results, eval=TRUE-------------------------------------------------- result.table <- getResult(meth.qtl.res) head(result.table) anno.meth <- getAnno(meth.qtl.res,"meth") head(anno.meth) anno.geno <- getAnno(meth.qtl.res,"geno") head(anno.geno) ## ----plots,eval=TRUE, include=TRUE-------------------------------------------- result.table <- result.table[order(result.table$P.value,decreasing=FALSE),] qtlPlotSNPCpGInteraction(imp.data,result.table$CpG[1],result.table$SNP[1]) qtlDistanceScatterplot(meth.qtl.res) ## ----interpretation, eval=TRUE, include=TRUE, warning=FALSE------------------- res <- qtlBaseSubstitutionEnrichment(meth.qtl.res) ## ----list, eval=TRUE, warning=FALSE------------------------------------------- meth.qtl.res.2 <- loadMethQTLResult(system.file("extdata","MethQTLResult_chr18",package="MAGAR")) meth.qtl.list <- list(First=meth.qtl.res,Second=meth.qtl.res.2) qtlVennPlot(meth.qtl.list,out.folder=getwd()) qtlUpsetPlot(meth.qtl.list,type = "cor.block") spec.first <- getSpecificQTL(meth.qtl.list$First,meth.qtl.list[-1]) ## ----cluster, eval=FALSE------------------------------------------------------ # qtlSetOption(cluster.config = c(h_vmem="60G",mem_free="20G")) # qtlSetOption(rscript.path = "/usr/bin/Rscript") # meth.qtl.res <- doMethQTL(meth.qtl = imp.data, # cluster.submit = T)