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feature/MSA_Support #64

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deb2502
Code cleanup
bariskalem Feb 13, 2024
9d8108d
Fix typos
bariskalem Feb 17, 2024
d453743
Merge branch 'epigen:master' into master
bariskalem May 22, 2024
c615a26
Implement Illumina MSA support
bariskalem Apr 10, 2025
8d30f14
remove a comment
bariskalem Apr 10, 2025
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2 changes: 1 addition & 1 deletion R/CNV.R
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Expand Up @@ -61,7 +61,7 @@ getGLADProfiles<-function(rnb.set,refbased=TRUE){

annot <- annotation(rnb.set)
target <- rnb.set@target
if(target %in% c("probes27","probes450","probesEPIC", "probesEPICv2")){
if(target %in% c("probes27","probes450","probesEPIC", "probesEPICv2", "probesMSA")){
target <- "probes450"
}
cnv.reference.data<-rnb.get.cnv.annotations(target)
Expand Down
2 changes: 2 additions & 0 deletions R/RnBSet-class.R
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Expand Up @@ -1177,6 +1177,8 @@ setMethod("mergeSamples", signature(object = "RnBSet"),
platform<-"EPIC"
}else if (object@target=="probesEPICv2"){
platform<-"EPICv2"
}else if (object@target=="probesMSA"){
platform<-"MSA"
}else if (object@target=="probes450"){
platform<-"450k"
}else if(object@target=="probes27"){
Expand Down
32 changes: 27 additions & 5 deletions R/RnBeadRawSet-class.R
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Expand Up @@ -173,7 +173,8 @@ RnBeadRawSet<-function(
beta.offset=100,
summarize.bead.counts=TRUE,
summarize.regions=TRUE,
region.types = rnb.region.types.for.analysis(ifelse(platform=="MMBC", "mm10", ifelse(target=="probesEPICv2", "hg38", rnb.getOption("assembly")))), ## TODO: Implement assembly selection
region.types = rnb.region.types.for.analysis(ifelse(platform=="MMBC", "mm10",
ifelse(target=="probesEPICv2"|| target=="probesMSA", "hg38", rnb.getOption("assembly")))), ## TODO: Implement assembly selection
useff=rnb.getOption("disk.dump.big.matrices"),
ffcleanup=FALSE){

Expand Down Expand Up @@ -252,6 +253,9 @@ RnBeadRawSet<-function(
}else if (platform =="EPICv2") {
target <- "probesEPICv2"
assembly <- "hg38"
}else if (platform =="MSA") {
target <- "probesMSA"
assembly <- "hg38"
}else if (platform =="450k") {
target <- "probes450"
assembly <- ifelse(genome.assembly == "hg19", "hg19", "hg38")
Expand Down Expand Up @@ -422,6 +426,8 @@ setAs("MethyLumiSet", "RnBeadRawSet",
platform="EPIC"
}else if(annotation(from)=="IlluminaMethylationEPICv2"){
platform="EPICv2"
}else if(annotation(from)=="IlluminaMethylationScreeningArray"){
platform="MSA"
}else if(annotation(from)=="IlluminaHumanMethylation450k"){
platform="450k"
}else if(annotation(from)=="IlluminaHumanMethylation27k"){
Expand Down Expand Up @@ -507,6 +513,9 @@ setAs("RnBeadRawSet","MethyLumiSet",
}else if(from@target == "probesEPICv2"){
probeIDs<-rnb.get.annotation("controlsEPICv2", assembly = "hg38")[,"Target"]
probeIDs<-paste(probeIDs, unlist(sapply(table(probeIDs)[unique(probeIDs)], seq, from=1 )), sep=".")
}else if(from@target == "probesMSA"){
probeIDs<-rnb.get.annotation("controlsMSA", assembly = "hg38")[,"Target"]
probeIDs<-paste(probeIDs, unlist(sapply(table(probeIDs)[unique(probeIDs)], seq, from=1 )), sep=".")
}else if(from@target == "probes450"){
probeIDs<-rnb.get.annotation("controls450")[,"Target"]
probeIDs<-paste(probeIDs, unlist(sapply(table(probeIDs)[unique(probeIDs)], seq, from=1 )), sep=".")
Expand All @@ -521,6 +530,8 @@ setAs("RnBeadRawSet","MethyLumiSet",
annotation(mset@QC) <- "IlluminaMethylationEPIC"
}else if(from@target == "probesEPICv2"){
annotation(mset@QC) <- "IlluminaMethylationEPICv2"
}else if(from@target == "probesMSA"){
annotation(mset@QC) <- "IlluminaMethylationScreeningArray"
}else if(from@target == "probes450"){
annotation(mset@QC) <- "IlluminaHumanMethylation450k"
}else if(from@target == "probes27"){
Expand All @@ -532,6 +543,8 @@ setAs("RnBeadRawSet","MethyLumiSet",
annotation(mset) <- "IlluminaMethylationEPIC"
}else if(from@target == "probesEPICv2"){
annotation(mset) <- "IlluminaMethylationEPICv2"
}else if(from@target == "probesMSA"){
annotation(mset) <- "IlluminaMethylationScreeningArray"
}else if(from@target == "probes450"){
annotation(mset) <- "IlluminaHumanMethylation450k"
}else if(from@target == "probes27"){
Expand All @@ -558,7 +571,10 @@ setAs("RGChannelSet", "RnBeadRawSet", function(from, to) {
} else if (assay.name == "IlluminaHumanMethylationEPICv2") {
assay.name <- "probesEPICv2"
platform.name <- "EPICv2"
} else if (assay.name == "IlluminaHumanMethylation450k") {
} else if (assay.name == "IlluminaHumanMethylationScreeningArray") {
assay.name <- "probesMSA"
platform.name <- "MSA"
} else if (assay.name == "IlluminaHumanMethylation450k") {
assay.name <- "probes450"
platform.name <- "450k"
} else if (assay.name == "IlluminaHumanMethylation27k") {
Expand All @@ -569,15 +585,16 @@ setAs("RGChannelSet", "RnBeadRawSet", function(from, to) {
}

## Use RnBeads' mapping from probe IDs to addresses
probes.all <- rnb.get.annotation(assay.name, ifelse(assay.name=="probesEPICv2", "hg38", rnb.getOption("assembly"))) ## TODO: Impove genome build selection
is.EPICv2.or.MSA <- ifelse(assay.name == "probesEPICv2" || assay.name == "probesMSA", TRUE, FALSE)
probes.all <- rnb.get.annotation(assay.name, ifelse(is.EPICv2.or.MSA, "hg38", rnb.getOption("assembly"))) ## TODO: Impove genome build selection
probes.all <- lapply(probes.all, function(x) {
result <- as.data.frame(mcols(x)[, c("Design", "Color", "AddressA", "AddressB")])
rownames(result) <- names(x)
result
}
)
probes.all <- do.call(rbind, unname(probes.all))
controls.all <- rnb.get.annotation(sub("^probes", "controls", assay.name), ifelse(assay.name=="probesEPICv2", "hg38", rnb.getOption("assembly"))) ## TODO: Impove genome build selection
controls.all <- rnb.get.annotation(sub("^probes", "controls", assay.name), ifelse(is.EPICv2.or.MSA, "hg38", rnb.getOption("assembly"))) ## TODO: Impove genome build selection
controls.all <- controls.all[, "ID"]

## Extract data on signals
Expand Down Expand Up @@ -674,7 +691,8 @@ setAs("RnBeadRawSet", "RGChannelSet", function(from, to){
# probes.all <- do.call(rbind, unname(probes.all))
probes.all <- annotation(from)[,c("Design", "Color", "AddressA", "AddressB")]
genome.assembly<-rnb.getOption("assembly")
controls.all <- rnb.get.annotation(sub("^probes", "controls", assay.name), ifelse(assay.name=="probesEPICv2", "hg38", genome.assembly))
is.EPICv2.or.MSA<-ifelse(assay.name == "probesEPICv2" || assay.name == "probesMSA", TRUE, FALSE)
controls.all <- rnb.get.annotation(sub("^probes", "controls", assay.name), ifelse(is.EPICv2.or.MSA, "hg38", genome.assembly))
controls.all <- controls.all[, "ID"]

# Obtain methylated and unmethylated intensities
Expand Down Expand Up @@ -747,6 +765,8 @@ setAs("RnBeadRawSet", "RGChannelSet", function(from, to){
anno <- "IlluminaHumanMethylationEPIC"
}else if(assay.name %in% "probesEPICv2"){
anno <- "IlluminaHumanMethylationEPICv2"
}else if(assay.name %in% "probesMSA"){
anno <- "IlluminaHumanMethylationScreeningArray"
}else if(assay.name %in% "probes450"){
anno <- "IlluminaHumanMethylation450k"
}else if(assay.name %in% "probes27"){
Expand Down Expand Up @@ -1305,6 +1325,8 @@ intensities.by.color<-function(raw.set,
if (add.controls) {
if (raw.set@target == "probesEPICv2") {
ncd <- rnb.get.annotation("controlsEPICv2", assembly = "hg38")
} else if (raw.set@target == "probesMSA") {
ncd <- rnb.get.annotation("controlsMSA", assembly = "hg38")
} else {
ncd <- rnb.get.annotation(ifelse(raw.set@target == "probesEPIC", "controlsEPIC", "controls450"))
}
Expand Down
6 changes: 5 additions & 1 deletion R/RnBeadSet-class.R
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Expand Up @@ -136,14 +136,15 @@ setMethod("initialize", "RnBeadSet",
.Object@qc<-qc

genome.assembly<-rnb.getOption("assembly")
is.EPICv2.or.MSA<-ifelse(target == "probesEPICv2" || target == "probesMSA", TRUE, FALSE)

callNextMethod(.Object,
pheno=pheno,
sites=sites,
meth.sites=meth.sites,
covg.sites=covg.sites,
status=status,
assembly=ifelse(target=="probesMMBC", "mm10", ifelse(target=="probesEPICv2", "hg38", genome.assembly)),
assembly=ifelse(target=="probesMMBC", "mm10", ifelse(is.EPICv2.or.MSA, "hg38", genome.assembly)),
target=target
)

Expand Down Expand Up @@ -246,6 +247,9 @@ RnBeadSet<-function(
} else if (platform == "EPICv2") {
target <- "probesEPICv2"
assembly <- "hg38"
} else if (platform == "MSA") {
target <- "probesMSA"
assembly <- "hg38"
} else if (platform == "450k") {
target <- "probes450"
assembly <- ifelse(genome.assembly == "hg19", "hg19", "hg38")
Expand Down
25 changes: 22 additions & 3 deletions R/annotations.R
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Expand Up @@ -98,7 +98,24 @@ EPIC.CONTROL.TARGETS <- c(
"staining" = "STAINING",
"target removal" = "TARGET REMOVAL")

EPICv2.CONTROL.TARGETS <- c( ## TODO: Not validated for EPIC v2 (Most likely it's compatible)
EPICv2.CONTROL.TARGETS <- c(
"bisulfite conversion I" = "BISULFITE CONVERSION I",
"bisulfite conversion II" = "BISULFITE CONVERSION II",
"extension" = "EXTENSION",
"hybridization" = "HYBRIDIZATION",
"negative control" = "NEGATIVE",
"non-polymorphic" = "NON-POLYMORPHIC",
"norm A" = "NORM_A",
"norm C" = "NORM_C",
"norm G" = "NORM_G",
"norm T" = "NORM_T",
"restoration" = "RESTORATION",
"specificity I" = "SPECIFICITY I",
"specificity II" = "SPECIFICITY II",
"staining" = "STAINING",
"target removal" = "TARGET REMOVAL")

MSA.CONTROL.TARGETS <- c( ## TODO: Not validated for MSA (Most likely it's compatible)
"bisulfite conversion I" = "BISULFITE CONVERSION I",
"bisulfite conversion II" = "BISULFITE CONVERSION II",
"extension" = "EXTENSION",
Expand Down Expand Up @@ -766,7 +783,7 @@ rnb.get.assemblies <- function() {
#' rnb.get.annotation("promoters")
#' }
rnb.get.annotation <- function(type = "CpG", assembly = "hg19") {
if (type == "probesEPICv2" || type == "controlsEPICv2") {
if (type == "probesEPICv2" || type == "controlsEPICv2" || type == "probesMSA" || type == "controlsMSA") {
assembly = "hg38"
}

Expand Down Expand Up @@ -1364,7 +1381,7 @@ rnb.get.chromosomes <- function(assembly = "hg19") {
#' Extracts all control probe types in the HumanMethylation450 assay.
#'
#' @param target A singleton of type \code{character}, specifying the microarray platform.
#' \code{"probesEPICv2"},\code{"probesEPIC"},\code{"probes450"} and \code{"probes27"} correspond to MethylationEPICv2,
#' \code{"probesEPICv2"},\code{"probesMSA"},\code{"probesEPIC"},\code{"probes450"} and \code{"probes27"} correspond to MethylationEPICv2,
#' Methylation EPIC, HumanMethylation450, and HumanMethylation27 microarrays respectively.
#'
#' @return \code{character} vector of control targets.
Expand All @@ -1380,6 +1397,8 @@ rnb.infinium.control.targets <- function(target="probes450") {
return(EPIC.CONTROL.TARGETS)
}else if(target=="probesEPICv2"){
return(EPICv2.CONTROL.TARGETS)
}else if(target=="probesMSA"){
return(MSA.CONTROL.TARGETS)
}else if(target=="probes450"){
return(HM450.CONTROL.TARGETS)
}else if(target=="probes27"){
Expand Down
1 change: 0 additions & 1 deletion R/batch.R
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Expand Up @@ -707,7 +707,6 @@ rnb.section.dreduction.internal <- function(report, pcoordinates, sample.phenoty
} else {
report <- rnb.add.section(report, "Low-dimensional Representation", stext)
}

## Mention that only some sites and/or regions are selected
if (!is.null(attr(pcoordinates, "selected"))) {
selected <- attr(pcoordinates, "selected")
Expand Down
5 changes: 5 additions & 0 deletions R/batch.quality.R
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Expand Up @@ -59,6 +59,11 @@ rnb.execute.batch.qc <- function(rnb.set, pcoordinates, permutations = NULL) {
id.col<-"ID"
type.col<-"Target"
ctrls<-"controlsEPICv2"
} else if(rnb.set@target=="probesMSA"){
CONTROL.TYPES <- rnb.infinium.control.targets("probesMSA")[c(1:4, 6, 11:14)]
id.col<-"ID"
type.col<-"Target"
ctrls<-"controlsMSA"
} else if(rnb.set@target=="probes450"){
CONTROL.TYPES <- rnb.infinium.control.targets("probes450")[c(1:4, 6, 11:14)]
id.col<-"ID"
Expand Down
3 changes: 2 additions & 1 deletion R/combining.R
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Expand Up @@ -122,6 +122,7 @@ rnb.combine.pheno <- function(dataset1, dataset2) {
#' @author Yassen Assenov
#' @export
rnb.combine.arrays <- function(dataset1, dataset2, type="common") {
## TODO: Update for MSA
if (!inherits(dataset1, "RnBeadSet")) {
stop("Invalid value for dataset1")
}
Expand All @@ -132,7 +133,7 @@ rnb.combine.arrays <- function(dataset1, dataset2, type="common") {
stop("Incompatible assemblies")
}
i <- c(dataset1@target, dataset2@target)
common.platform <- c("probesEPICv2" = "EPICv2", "probesEPIC" = "EPIC", "probes450" = "450k", "probes27" = "27k") ## TODO: Validate for EPICv2 (on EPICv1 ?)
common.platform <- c("probesEPICv2" = "EPICv2", "probesEPIC" = "EPIC", "probes450" = "450k", "probes27" = "27k")
if (!(i[1] %in% names(common.platform))) {
stop("Unsupported platform for dataset1")
}
Expand Down
30 changes: 17 additions & 13 deletions R/controlPlots.R
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Expand Up @@ -61,6 +61,8 @@ rnb.plot.control.boxplot <- function(
meta <- rnb.get.annotation("controlsEPIC", assembly = "hg19")
}else if(rnb.set@target=="probesEPICv2"){
meta <- rnb.get.annotation("controlsEPICv2", assembly = "hg38")
}else if(rnb.set@target=="probesMSA"){
meta <- rnb.get.annotation("controlsMSA", assembly = "hg38")
}else if(rnb.set@target=="probes450"){
meta <- rnb.get.annotation("controls450", assembly = "hg19")
}else if(rnb.set@target=="probes27"){
Expand All @@ -73,6 +75,8 @@ rnb.plot.control.boxplot <- function(
types<-rnb.infinium.control.targets(rnb.set@target)[c(14,4,3,15,1:2,12:13,6,11)]
}else if(rnb.set@target=="probesEPICv2"){
types<-rnb.infinium.control.targets(rnb.set@target)[c(14,4,3,15,1:2,12:13,6,11)]
}else if(rnb.set@target=="probesMSA"){
types<-rnb.infinium.control.targets(rnb.set@target)[c(14,4,3,15,1:2,12:13,6,11)]
}else if(rnb.set@target=="probes450"){
types<-rnb.infinium.control.targets(rnb.set@target)[c(13,4,3,14,1:2,11:12,6)]
}else if(rnb.set@target=="probes27"){
Expand All @@ -85,12 +89,12 @@ rnb.plot.control.boxplot <- function(
warning("Unoptimized probe type, plotting performance may be decreased")
}

if(rnb.set@target=="probes450" || rnb.set@target=="probesEPIC" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesEPICv2"){
if(rnb.set@target=="probes450" || rnb.set@target=="probesEPIC" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMSA"){
rownames(meta)<-meta[["ID"]]
### TODO: Remove the following passage
### for testing purposes only!
if(rnb.set@target=="probesEPIC" || rnb.set@target=="probesEPICv2"){
meta<-rnb.update.controlsEPIC.enrich(meta) ## TODO: Not validated for EPICv2
if(rnb.set@target=="probesEPIC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMSA"){
meta<-rnb.update.controlsEPIC.enrich(meta) ## TODO: Not validated for EPICv2 & MSA
}
meta <- meta[type == meta[["Target"]], ]
ids<-as.character(meta[["ID"]])
Expand Down Expand Up @@ -125,7 +129,7 @@ rnb.plot.control.boxplot <- function(

scales<-lapply(qc(rnb.set), get.unified.scale)

if(rnb.set@target=="probes450" || rnb.set@target=="probesEPIC" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesEPICv2"){
if(rnb.set@target=="probes450" || rnb.set@target=="probesEPIC" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMSA"){
## Shorten the words describing probe's expected intensity
INTENSITIES <- c("Background" = "Bgnd", "High" = "High", "Low" = "Low", "Medium" = "Med")
levels(meta[, "Expected Intensity"]) <- INTENSITIES[levels(meta[, "Expected Intensity"])]
Expand Down Expand Up @@ -220,14 +224,14 @@ rnb.plot.negative.boxplot<- function(
...) {


if(rnb.set@target=="probesEPIC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMMBC" ){
if(rnb.set@target=="probesEPIC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesMSA"){
genome.assembly<-rnb.getOption("assembly")
meta <- rnb.get.annotation(gsub("probes", "controls", rnb.set@target), assembly=c("probesEPIC"=genome.assembly, "probesMMBC"="mm10", "probesEPICv2"="hg38")[rnb.set@target])
meta <- rnb.get.annotation(gsub("probes", "controls", rnb.set@target), assembly=c("probesEPIC"=genome.assembly, "probesMMBC"="mm10", "probesEPICv2"="hg38", "probesMSA"="hg38")[rnb.set@target])
## Extract intensities of the control probes
### TODO: Remove the following passage
### for testing purposes only!
if(rnb.set@target=="probesEPIC" || rnb.set@target=="probesEPICv2"){
meta<-rnb.update.controlsEPIC.enrich(meta) ## TODO: Not validated for EPICv2 (duplicate)
if(rnb.set@target=="probesEPIC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMSA"){
meta<-rnb.update.controlsEPIC.enrich(meta) ## TODO: Not validated for EPICv2 & MSA (duplicate)
}
meta <- meta["NEGATIVE" == meta[["Target"]], ]
ids<-as.character(meta[["ID"]])
Expand Down Expand Up @@ -367,9 +371,9 @@ rnb.plot.control.barplot<-function(
{


if(rnb.set@target=="probesEPIC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMMBC"){
if(rnb.set@target=="probesEPIC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesMSA"){
genome.assembly<-rnb.getOption("assembly") ## TODO: Improve genome build selection
control.meta.data <- rnb.get.annotation(gsub("probes", "controls", rnb.set@target), assembly=c("probesEPIC"=genome.assembly, "probesEPICv2"="hg38", "probesMMBC"="mm10")[rnb.set@target])
control.meta.data <- rnb.get.annotation(gsub("probes", "controls", rnb.set@target), assembly=c("probesEPIC"=genome.assembly, "probesEPICv2"="hg38", "probesMSA"="hg38", "probesMMBC"="mm10")[rnb.set@target])
### TODO: Remove the following passage
### for testing purposes only!
#if(rnb.set@target=="probesEPIC"){
Expand Down Expand Up @@ -438,7 +442,7 @@ rnb.plot.control.barplot<-function(

## get meta information

if(rnb.set@target=="probes450" || rnb.set@target=="probesEPIC" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesEPICv2"){
if(rnb.set@target=="probes450" || rnb.set@target=="probesEPIC" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMSA"){
meta<-subset(control.meta.data, ID==id)
}else if(rnb.set@target=="probes27"){
meta<-subset(control.meta.data, Address==id)
Expand All @@ -465,7 +469,7 @@ rnb.plot.control.barplot<-function(

### plot green channel

if(rnb.set@target=="probes450" || rnb.set@target=="probesEPIC" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesEPICv2"){
if(rnb.set@target=="probes450" || rnb.set@target=="probesEPIC" || rnb.set@target=="probesMMBC" || rnb.set@target=="probesEPICv2" || rnb.set@target=="probesMSA"){
main_txt_grn<-paste(probe, meta[,"Description"], "green channel", if(meta[, "Evaluate Green"]=="+") meta[, "Expected Intensity"] else "Background", sep=": ")
main_txt_red<-paste(probe, meta[,"Description"], "red channel",if(meta[, "Evaluate Red"]=="+") meta[, "Expected Intensity"] else "Background", sep=": ")
}else{
Expand Down Expand Up @@ -531,7 +535,7 @@ rnb.plot.control.barplot<-function(
#' @author Yassen Assenov
#' @noRd
rnb.get.snp.matrix <- function(dataset, threshold.nas = 1) {
if (dataset@target %in% c("probes450", "probesEPIC", "probesMMBC", "probesEPICv2")) {
if (dataset@target %in% c("probes450", "probesEPIC", "probesMMBC", "probesEPICv2", "probesMSA")) {
result <- meth(dataset, row.names=TRUE)
result <- result[grep("^rs", rownames(result)), , drop = FALSE]
} else if (dataset@target == "probes27") {
Expand Down
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