inst/doc/MEAL.R

## ----setup, include=FALSE--------------------------------------------------
knitr::opts_chunk$set(message = FALSE, warning = FALSE)

## ---- message = FALSE------------------------------------------------------
library(MEAL)
library(MultiDataSet)
library(minfiData)
library(minfi)
library(ggplot2)

data("MsetEx")

## ----subset Methy----------------------------------------------------------
meth <- mapToGenome(ratioConvert(MsetEx))
rowData(meth) <- getAnnotation(meth)[, -c(1:3)]

## Remove probes measuring SNPs
meth <- dropMethylationLoci(meth)

## Remove probes with SNPs
meth <- dropLociWithSnps(meth)

## Remove probes with NAs
meth <- meth[!apply(getBeta(meth), 1, function(x) any(is.na(x))), ]

## ----Pipeline,  warning=FALSE, eval = FALSE--------------------------------
#  res <- runPipeline(set = meth, variable_names = "status")

## ----Pipeline Adj,  warning=FALSE------------------------------------------
resAdj <- runPipeline(set = meth, variable_names = "status", 
                      covariable_names = "age")
resAdj

## --------------------------------------------------------------------------
names(resAdj)

## --------------------------------------------------------------------------
head(getAssociation(resAdj, "DiffMean"))
head(getAssociation(resAdj, "DiffVar"))
head(getAssociation(resAdj, "bumphunter"))
head(getAssociation(resAdj, "blockFinder"))
head(getAssociation(resAdj, "dmrcate"))

## ----get Probe Res several coefs-------------------------------------------
head(getProbeResults(resAdj, rid = 1, coef = 2:3, 
                     fNames = c("chromosome", "start")))

## ----getGeneVals-----------------------------------------------------------
getGeneVals(resAdj, "ARMS2", genecol = "UCSC_RefGene_Name", fNames = c("chromosome", "start"))

## ----Manhattan 1-----------------------------------------------------------
targetRange <- GRanges("23:13000000-23000000")
plot(resAdj, rid = "DiffMean", type = "manhattan", highlight = targetRange)
plot(resAdj, rid = "DiffMean", type = "manhattan", subset = targetRange)

## ----Manhattan 2-----------------------------------------------------------
plot(resAdj, rid = "DiffMean", type = "manhattan", suggestiveline = 3, 
     genomewideline = 6, main = "My custom Manhattan")
abline(h = 13, col = "yellow")

## ----Volcano 1-------------------------------------------------------------
plot(resAdj, rid = "DiffMean", type = "volcano", tPV = 14, tFC = 0.4, 
     show.labels = FALSE) + ggtitle("My custom Volcano")

## ----QQ--------------------------------------------------------------------
plot(resAdj, rid = "DiffMean", type = "qq") + ggtitle("My custom QQplot")

## ----Plot_Features, warning = FALSE----------------------------------------
plotFeature(set = meth, feat = "cg17547524", variables = "sex") + 
  ggtitle("Diff Means")
plotFeature(set = meth, feat = "cg02939019", variables = "sex") + 
  ggtitle("Diff Vars")

## ----Regional plot 1-------------------------------------------------------
targetRange <- GRanges("chrX:13000000-14000000")
plotRegion(resAdj, targetRange)

## ----Regional plot 2-------------------------------------------------------
plotRegion(resAdj, targetRange, results = c("DiffMean", "bumphunter"), 
           tPV = 10)

## ----DiffMean, eval = FALSE------------------------------------------------
#  resDM <- runDiffMeanAnalysis(set = meth, model = ~ status)

## ----DiffVar, eval = FALSE-------------------------------------------------
#  resDV <- runDiffVarAnalysis(set = meth, model = ~ status, coefficient = 2)

## ----Bumphunter, eval = FALSE----------------------------------------------
#  resBH <- runBumphunter(set = meth, model = ~ status, coefficient = 2)

## ----blockFinder, eval = FALSE---------------------------------------------
#  resBF <- runBlockFinder(set = meth, model = ~ status, coefficient = 2)

## ----DMRcate, eval = FALSE-------------------------------------------------
#  resDC <- runDMRcate(set = meth, model = ~ status, coefficient = 2)

## ----RDA-------------------------------------------------------------------
targetRange <- GRanges("chrX:13000000-23000000")
resRDA <- runRDA(set = meth, model = ~ status, range = targetRange)

## ----RDA res---------------------------------------------------------------
getAssociation(resRDA, rid = "RDA")

## ----getRDAresults---------------------------------------------------------
getRDAresults(resRDA)

## ----topRDAhits------------------------------------------------------------
topRDAhits(resRDA)

## ----plotRDA---------------------------------------------------------------
plotRDA(object = resRDA, pheno = colData(meth)[, "status", drop = FALSE])

## ----plotRDA 2-------------------------------------------------------------
plotRDA(object = resRDA, pheno = colData(meth)[, "status", drop = FALSE])
abline(h = -1)

## ----session Info----------------------------------------------------------
sessionInfo()

Try the MEAL package in your browser

Any scripts or data that you put into this service are public.

MEAL documentation built on Nov. 1, 2018, 5:01 a.m.