missMethyl 1.40.0
The missMethyl package contains functions to analyse methylation data from Illumina’s HumanMethylation450 and MethylationEPIC beadchip. These arrays are a cost-effective alternative to whole genome bisulphite sequencing, and as such are widely used to profile DNA methylation. Specifically, missMethyl contains functions to perform SWAN normalisation (Maksimovic, Gordon, and Oshlack 2012),perform differential methylation analysis using RUVm (Maksimovic et al. 2015), differential variability analysis (Phipson and Oshlack 2014) and gene set enrichment analysis (Phipson, Maksimovic, and Oshlack 2016). As our lab’s research into specialised analyses of these arrays continues we anticipate that the package will be updated with new functions.
Raw data files are in IDAT format, which can be read into R using the
minfi package (Aryee et al. 2014). Statistical analyses are
usually performed on M-values, and \(\beta\) values are used for visualisation,
both of which can be extracted from MethylSet
data objects, which is a class
of object created by minfi. For detecting
differentially variable CpGs we recommend that the analysis is performed on
M-values. All analyses described here are performed at the CpG site level.
The missMethyl package has been updated to support Illumina’s MethylationEPIC v2.0 beadchip. This array contains replicate probes which map to the same CpG dinucleotides. We recommend filtering these replicates prior to analysis with the missMethyl package using the DMRcate package. An example of this is shown in this vignette.
We will use the data in the minfiData package to
demonstrate the functions in missMethyl.
The example dataset has 6 samples across two slides. There are 3 cancer samples
and 3 normal sample. The sample information is in the targets file. An
essential column in the targets file is the Basename
column which tells us
where the idat files to be read in are located. The R commands to read in the
data are taken from the minfi User’s Guide. For
additional details on how to read the IDAT files into R, as well as information
regarding quality control please refer to the minfi
User’s Guide.
library(missMethyl)
library(limma)
library(minfi)
library(minfiData)
baseDir <- system.file("extdata", package = "minfiData")
targets <- read.metharray.sheet(baseDir)
## [1] "/home/biocbuild/bbs-3.20-bioc/R/site-library/minfiData/extdata/SampleSheet.csv"
targets[,1:9]
## Sample_Name Sample_Well Sample_Plate Sample_Group Pool_ID person age sex
## 1 GroupA_3 H5 <NA> GroupA <NA> id3 83 M
## 2 GroupA_2 D5 <NA> GroupA <NA> id2 58 F
## 3 GroupB_3 C6 <NA> GroupB <NA> id3 83 M
## 4 GroupB_1 F7 <NA> GroupB <NA> id1 75 F
## 5 GroupA_1 G7 <NA> GroupA <NA> id1 75 F
## 6 GroupB_2 H7 <NA> GroupB <NA> id2 58 F
## status
## 1 normal
## 2 normal
## 3 cancer
## 4 cancer
## 5 normal
## 6 cancer
targets[,10:12]
## Array Slide
## 1 R02C02 5723646052
## 2 R04C01 5723646052
## 3 R05C02 5723646052
## 4 R04C02 5723646053
## 5 R05C02 5723646053
## 6 R06C02 5723646053
## Basename
## 1 /home/biocbuild/bbs-3.20-bioc/R/site-library/minfiData/extdata/5723646052/5723646052_R02C02
## 2 /home/biocbuild/bbs-3.20-bioc/R/site-library/minfiData/extdata/5723646052/5723646052_R04C01
## 3 /home/biocbuild/bbs-3.20-bioc/R/site-library/minfiData/extdata/5723646052/5723646052_R05C02
## 4 /home/biocbuild/bbs-3.20-bioc/R/site-library/minfiData/extdata/5723646053/5723646053_R04C02
## 5 /home/biocbuild/bbs-3.20-bioc/R/site-library/minfiData/extdata/5723646053/5723646053_R05C02
## 6 /home/biocbuild/bbs-3.20-bioc/R/site-library/minfiData/extdata/5723646053/5723646053_R06C02
rgSet <- read.metharray.exp(targets = targets)
The data is now an RGChannelSet
object and needs to be normalised and
converted to a MethylSet
object.
When using MethylationEPIC v2.0 datasets, the array and annotation details in
the RGChannelSet
object must be set manually.
### This code is not run within this vignette
# If using EPIC_V2, please run these lines:
annotation(rgSet)["array"] = "IlluminaHumanMethylationEPICv2"
annotation(rgSet)["annotation"] = "20a1.hg38"
### End of not run
SWAN (subset-quantile within array normalization) is a within-array normalization method for Illumina 450k & EPIC BeadChips. Technical differencs have been demonstrated to exist between the Infinium I and Infinium II assays on a single Illumina HumanMethylation array (Bibikova et al. 2011, @Dedeurwaerder2011). Using the SWAN method substantially reduces the technical variability between the assay designs whilst maintaining important biological differences. The SWAN method makes the assumption that the number of CpGs within the 50bp probe sequence reflects the underlying biology of the region being interrogated. Hence, the overall distribution of intensities of probes with the same number of CpGs in the probe body should be the same regardless of assay type. The method then uses a subset quantile normalization approach to adjust the intensities of each array (Maksimovic, Gordon, and Oshlack 2012).
SWAN
can take a MethylSet
, RGChannelSet
or MethyLumiSet
as input. It
should be noted that, in order to create the normalization subset, SWAN
randomly selects Infinium I and II probes that have one, two and three
underlying CpGs; as such, we recommend using set.seed
before to ensure that
the normalized intensities will be
identical, if the normalization is repeated.
The technical differences between Infinium I and II assay designs can result in aberrant \(\beta\) value distributions (Figure 1, panel “Raw”). Using SWAN corrects for the technical differences between the Infinium I and II assay designs and produces a smoother overall \(\beta\) value distribution (Figure 1, panel “SWAN”).
mSet <- preprocessRaw(rgSet)
mSetSw <- SWAN(mSet,verbose=TRUE)
## [SWAN] Preparing normalization subset
## 450k
## [SWAN] Normalizing methylated channel
## [SWAN] Normalizing array 1 of 6
## [SWAN] Normalizing array 2 of 6
## [SWAN] Normalizing array 3 of 6
## [SWAN] Normalizing array 4 of 6
## [SWAN] Normalizing array 5 of 6
## [SWAN] Normalizing array 6 of 6
## [SWAN] Normalizing unmethylated channel
## [SWAN] Normalizing array 1 of 6
## [SWAN] Normalizing array 2 of 6
## [SWAN] Normalizing array 3 of 6
## [SWAN] Normalizing array 4 of 6
## [SWAN] Normalizing array 5 of 6
## [SWAN] Normalizing array 6 of 6
par(mfrow=c(1,2), cex=1.25)
densityByProbeType(mSet[,1], main = "Raw")
densityByProbeType(mSetSw[,1], main = "SWAN")
Poor quality probes can be filtered out based on the detection p-value. For this example, to retain a CpG for further analysis, we require that the detection p-value is less than 0.01 in all samples.
detP <- detectionP(rgSet)
keep <- rowSums(detP < 0.01) == ncol(rgSet)
mSetSw <- mSetSw[keep,]
Now that the data has been SWAN
normalised we can extract \(\beta\) and
M-values from the object. We prefer to add an offset to the methylated
and unmethylated intensities when calculating M-values, hence we extract
the methylated and unmethylated channels separately and perform our own
calculation. For all subsequent analyses we use a random selection of
20000 CpGs to reduce computation time.
set.seed(10)
mset_reduced <- mSetSw[sample(1:nrow(mSetSw), 20000),]
meth <- getMeth(mset_reduced)
unmeth <- getUnmeth(mset_reduced)
Mval <- log2((meth + 100)/(unmeth + 100))
beta <- getBeta(mset_reduced)
dim(Mval)
## [1] 20000 6
par(mfrow=c(1,1))
plotMDS(Mval, labels=targets$Sample_Name, col=as.integer(factor(targets$status)))
legend("topleft",legend=c("Cancer","Normal"),pch=16,cex=1.2,col=1:2)
An MDS plot (Figure 2) is a good sanity check to make sure samples cluster together according to the main factor of interest, in this case, cancer and normal.
The MethylationEPIC v2.0 array contains replicate probes which map to the same CpG dinucleotides. We recommend filtering these replicate probes using the DMRcate package as shown below. Please see the [DMRcate](https://bioconductor.org/packages/3.20/DMRcate) EPICv2 vignette for more details.
### This code is not run within this vignette
# For EPIC_V2, please run these lines to remove replicate and non-cg probes:
# remove non-cg probes
Mval <- Mval[grepl("^cg", rownames(Mval)),]
# select replicate probes with best sensitivity
Mval <- DMRcate::rmPosReps(Mval, filter.strategy="sensitivity")
### End of not run
To test for differential methylation we use the limma
package (Smyth 2005), which employs an empirical Bayes framework based on
Guassian model theory. First we need to set up the design matrix.
There are a number of ways to do this, the most straightforward is directly from
the targets file. There are a number of variables, with the status
column
indicating cancer/normal samples. From the person
column of the targets
file, we see that the cancer/normal samples are matched, with 3 individuals
each contributing both a cancer and normal sample. Since the
limma model framework can handle any experimental
design which can be summarised by a design matrix, we can take into account the
paired nature of the data in the analysis. For more complicated experimental
designs, please refer to the limma User’s Guide.
group <- factor(targets$status,levels=c("normal","cancer"))
id <- factor(targets$person)
design <- model.matrix(~id + group)
design
## (Intercept) idid2 idid3 groupcancer
## 1 1 0 1 0
## 2 1 1 0 0
## 3 1 0 1 1
## 4 1 0 0 1
## 5 1 0 0 0
## 6 1 1 0 1
## attr(,"assign")
## [1] 0 1 1 2
## attr(,"contrasts")
## attr(,"contrasts")$id
## [1] "contr.treatment"
##
## attr(,"contrasts")$group
## [1] "contr.treatment"
Now we can test for differential methylation using the lmFit
and eBayes
functions from limma. As input data we use the matrix of
M-values.
fit.reduced <- lmFit(Mval,design)
fit.reduced <- eBayes(fit.reduced, robust=TRUE)
The numbers of hyper-methylated (1) and hypo-methylated (-1) can be
displayed using the decideTests
function in limma
and the top 10 differentially methylated CpGs for cancer versus normal
extracted using topTable
.
summary(decideTests(fit.reduced))
## (Intercept) idid2 idid3 groupcancer
## Down 6966 0 120 577
## NotSig 3366 20000 19875 18950
## Up 9668 0 5 473
top<-topTable(fit.reduced,coef=4)
top
## logFC AveExpr t P.Value adj.P.Val B
## cg16969623 4.738630 -1.3299003 18.19044 5.173550e-06 0.02961263 4.437708
## cg24115221 4.263797 -0.4610231 16.36669 9.020982e-06 0.02961263 4.071486
## cg13692446 4.358674 0.3082280 15.78961 1.089203e-05 0.02961263 3.939795
## cg11334818 4.034771 0.9277920 15.28520 1.291378e-05 0.02961263 3.817612
## cg10341556 4.978126 -1.5761985 15.42154 1.331473e-05 0.02961263 3.783887
## cg17815252 3.691483 -2.3570265 14.67851 1.596482e-05 0.02961263 3.661210
## cg24331301 3.847282 -1.4302450 14.47935 1.714739e-05 0.02961263 3.607480
## cg26976732 3.848104 -0.9274223 14.35266 1.795372e-05 0.02961263 3.572657
## cg26328335 3.726501 0.3548518 14.15063 1.933427e-05 0.02961263 3.516070
## cg05621343 4.271503 -0.5600706 14.17489 1.946740e-05 0.02961263 3.509129
Note that since we performed our analysis on M-values, the logFC
and
AveExpr
columns are computed on the M-value scale. For interpretability
and visualisation we can look at the \(\beta\) values. The \(\beta\) values for
the top 4 differentially methylated CpGs shown in Figure 3.
cpgs <- rownames(top)
par(mfrow=c(2,2))
for(i in 1:4){
stripchart(beta[rownames(beta)==cpgs[i],]~design[,4],method="jitter",
group.names=c("Normal","Cancer"),pch=16,cex=1.5,col=c(4,2),ylab="Beta values",
vertical=TRUE,cex.axis=1.5,cex.lab=1.5)
title(cpgs[i],cex.main=1.5)
}
Like other platforms, 450k array studies are subject to unwanted technical variation such as batch effects and other, often unknown, sources of variation. The adverse effects of unwanted variation have been extensively documented in gene expression array studies and have been shown to be able to both reduce power to detect true differences and to increase the number of false discoveries. As such, when it is apparent that data is significantly affected by unwanted variation, it is advisable to perform an adjustment to mitigate its effects.
missMethyl provides a limma inspired interface to functions from the CRAN package ruv, which enable the removal of unwanted variation when performing a differential methylation analysis (Maksimovic et al. 2015).
RUVfit
uses the RUV-inverse method by default, as this does not require the
user to specify a \(k\) parameter. The ridged version of RUV-inverse is also
available by setting method = rinv
. The RUV-2 and RUV-4 functions can also
be used by setting method = ruv2
or method = ruv4
, respectively, and
specifying an appropriate value for k (number of components of unwanted
variation to remove) where \(0 \leq k < no. samples\).
All of the methods rely on negative control features to accurately estimate the components of unwanted variation. Negative control features are probes/genes/etc. that are known a priori to not truly be associated with the biological factor of interest, but are affected by unwanted variation. For example, in a microarray gene expression study, these could be house-keeping genes or a set of spike-in controls. Negative control features are extensively discussed in Gagnon-Bartsch and Speed (2012) and Gagnon-Bartsch et al. (2013). Once the unwanted factors are accurately estimated from the data, they are adjusted for in the linear model that describes the differential analysis.
If the negative control features are not known a priori, they can be identified empirically. This can be achieved via a 2-stage approach, RUVm. Stage 1 involves performing a differential methylation analysis using RUV-inverse (by default) and the 613 Illumina negative controls (INCs) as negative control features. This will produce a list of CpGs ranked by p-value according to their level of association with the factor of interest. This list can then be used to identify a set of empirical control probes (ECPs), which will capture more of the unwanted variation than using the INCs alone. ECPs are selected by designating a proportion of the CpGs least associated with the factor of interest as negative control features; this can be done based on either an FDR cut-off or by taking a fixed percentage of probes from the bottom of the ranked list. Stage 2 involves performing a second differential methylation analysis on the original data using RUV-inverse (by default) and the ECPs. For simplicity, we are ignoring the paired nature of the cancer and normal samples in this example.
# get M-values for ALL probes
meth <- getMeth(mSet)
unmeth <- getUnmeth(mSet)
M <- log2((meth + 100)/(unmeth + 100))
### This code is not run within this vignette
# For EPIC_V2, please run these lines to remove replicate and non-cg probes:
# remove non-cg probes
M <- M[grepl("^cg", rownames(M)),]
# select replicate probes with best sensitivity
M <- DMRcate::rmPosReps(M, filter.strategy="sensitivity")
### End of not run
# setup the factor of interest
grp <- factor(targets$status, labels=c(0,1))
# extract Illumina negative control data
INCs <- getINCs(rgSet)
head(INCs)
## 5723646052_R02C02 5723646052_R04C01 5723646052_R05C02
## 13792480 -0.3299654 -1.0955482 -0.5266103
## 69649505 -1.0354488 -1.4943396 -1.0067050
## 34772371 -1.1286422 -0.2995603 -0.8192636
## 28715352 -0.5553373 -0.7599489 -0.7186973
## 74737439 -1.1169178 -0.8656399 -0.6429681
## 33730459 -0.7714684 -0.5622424 -0.7724825
## 5723646053_R04C02 5723646053_R05C02 5723646053_R06C02
## 13792480 -0.6374299 -1.116598 -0.4332793
## 69649505 -0.8854881 -1.586679 -0.9217329
## 34772371 -0.6895514 -1.161155 -0.6186795
## 28715352 -1.7903619 -1.348105 -1.0067259
## 74737439 -0.8872082 -1.064986 -0.9841833
## 33730459 -1.5623138 -2.079184 -1.0445246
# add negative control data to M-values
Mc <- rbind(M,INCs)
# create vector marking negative controls in data matrix
ctl1 <- rownames(Mc) %in% rownames(INCs)
table(ctl1)
## ctl1
## FALSE TRUE
## 485512 613
rfit1 <- RUVfit(Y = Mc, X = grp, ctl = ctl1) # Stage 1 analysis
rfit2 <- RUVadj(Y = Mc, fit = rfit1)
Now that we have performed an initial differential methylation analysis to rank the CpGs with respect to their association with the factor of interest, we can designate the CpGs that are least associated with the factor of interest based on FDR-adjusted p-value as ECPs.
top1 <- topRUV(rfit2, num=Inf, p.BH = 1)
head(top1)
## F.p F.p.BH p_X1.1 p.BH_X1.1 b_X1.1 sigma2
## cg04743961 3.516091e-07 0.01017357 3.516091e-07 0.01017357 -4.838190 0.10749571
## cg07155336 3.583107e-07 0.01017357 3.583107e-07 0.01017357 -5.887409 0.16002329
## cg20925841 3.730375e-07 0.01017357 3.730375e-07 0.01017357 -4.790211 0.10714494
## cg03607359 4.721205e-07 0.01017357 4.721205e-07 0.01017357 -4.394397 0.09636129
## cg10566121 5.238865e-07 0.01017357 5.238865e-07 0.01017357 -4.787914 0.11780108
## cg07655636 6.080091e-07 0.01017357 6.080091e-07 0.01017357 -4.571758 0.11201883
## var.b_X1.1 fit.ctl mean
## cg04743961 0.07729156 FALSE -2.31731496
## cg07155336 0.11505994 FALSE -1.27676413
## cg20925841 0.07703935 FALSE -0.87168892
## cg03607359 0.06928569 FALSE -2.19187147
## cg10566121 0.08470133 FALSE 0.03138961
## cg07655636 0.08054378 FALSE -1.29294851
ctl2 <- rownames(M) %in% rownames(top1[top1$p.BH_X1.1 > 0.5,])
table(ctl2)
## ctl2
## FALSE TRUE
## 172540 312972
We can then use the ECPs to perform a second differential methylation with RUV-inverse, which is adjusted for the unwanted variation estimated from the data.
# Perform RUV adjustment and fit
rfit3 <- RUVfit(Y = M, X = grp, ctl = ctl2) # Stage 2 analysis
rfit4 <- RUVadj(Y = M, fit = rfit3)
# Look at table of top results
topRUV(rfit4)
## F.p F.p.BH p_X1.1 p.BH_X1.1 b_X1.1 sigma2 var.b_X1.1 fit.ctl
## cg07155336 1e-24 1e-24 1e-24 1e-24 -5.769286 0.1668414 0.1349771 FALSE
## cg06463958 1e-24 1e-24 1e-24 1e-24 -5.733093 0.1668414 0.1349771 FALSE
## cg00024472 1e-24 1e-24 1e-24 1e-24 -5.662959 0.1668414 0.1349771 FALSE
## cg02040433 1e-24 1e-24 1e-24 1e-24 -5.651399 0.1668414 0.1349771 FALSE
## cg13355248 1e-24 1e-24 1e-24 1e-24 -5.595396 0.1668414 0.1349771 FALSE
## cg02467990 1e-24 1e-24 1e-24 1e-24 -5.592707 0.1668414 0.1349771 FALSE
## cg00817367 1e-24 1e-24 1e-24 1e-24 -5.527501 0.1668414 0.1349771 FALSE
## cg11396157 1e-24 1e-24 1e-24 1e-24 -5.487992 0.1668414 0.1349771 FALSE
## cg16306898 1e-24 1e-24 1e-24 1e-24 -5.466780 0.1668414 0.1349771 FALSE
## cg03735888 1e-24 1e-24 1e-24 1e-24 -5.396242 0.1668414 0.1349771 FALSE
## mean
## cg07155336 -1.2767641
## cg06463958 0.2776252
## cg00024472 -2.4445762
## cg02040433 -1.2918259
## cg13355248 -0.8483387
## cg02467990 -0.4154370
## cg00817367 -0.2911294
## cg11396157 -1.3800170
## cg16306898 -2.1469768
## cg03735888 -1.1527557
If the number of samples in your experiment is greater than the number of Illumina negative controls on the array platform used - 613 for 450k, 411 for EPIC - stage 1 of RUVm will not work. In such cases, we recommend performing a standard limma analysis in stage 1.
# setup design matrix
des <- model.matrix(~grp)
des