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Adapt convertArray method for EPICv2 chip. Fix a bug in convertArray … #289

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Adapt convertArray method for EPICv2 chip. Fix a bug in convertArray … #289

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59 changes: 46 additions & 13 deletions R/combineArrays.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,8 @@

outType <- match.arg(outType)
.isRGOrStop(rgSet)
stopifnot(.is450k(rgSet) || .isEPIC(rgSet))
# Make EPICv2 compatible | Add type EPICv2
stopifnot(.is450k(rgSet) || .isEPIC(rgSet) || .isEPICv2(rgSet))

array <- annotation(rgSet)["array"]
if (array == outType) stop("'rgSet' already in the 'outType' array type.")
Expand All @@ -54,44 +55,69 @@
commonNames <- intersect(probes1$Name, probes2$Name)
probes1 <- probes1[match(commonNames, probes1$Name), ]
probes2 <- probes2[match(commonNames, probes2$Name), ]
# Make EPICv2 compatible | EPICv2 remove different design probes
if (.isEPICv2(rgSet)){
Diff_Color_Indices <- which(probes1$Color != probes2$Color)
commonNames <- setdiff(commonNames, probes2$Name[Diff_Color_Indices])
Diff_ProbeSeqA_Indices <- which(probes1$ProbeSeqA != probes2$ProbeSeqA)
commonNames <- setdiff(commonNames, probes2$Name[Diff_ProbeSeqA_Indices])
probes1 <- probes1[match(commonNames, probes1$Name), ]
probes2 <- probes2[match(commonNames, probes2$Name), ]
}
stopifnot(all(probes1$Color == probes2$Color))
stopifnot(all(probes1$ProbeSeqA == probes2$ProbeSeqA))
stopifnot(all(probes1$ProbeSeqB == probes2$ProbeSeqB))
# Translating rgSet2 addresses to rgSet1 addresses
translate <- c(probes1$AddressA, probes1$AddressB)
names(translate) <- c(probes2$AddressA, probes2$AddressB)
wh <- which(rownames(rgSet) %in% names(translate))
rownames(rgSet)[wh] <- translate[rownames(rgSet)[wh]]
keepAddresses$I <- unname(translate)
# Fix Bug | Save relation between rgSet2 addresses and rgSet1 addresses. Don't change rownames(rgSet) here
keepAddresses$I <- names(translate)
translate_all <- translate

# Probes of Type II
probes1 <- getProbeInfo(manifest1, type = "II")
probes2 <- getProbeInfo(manifest2, type = "II")
commonNames <- intersect(probes1$Name, probes2$Name)
probes1 <- probes1[match(commonNames, probes1$Name),]
probes2 <- probes2[match(commonNames, probes2$Name),]
# Make EPICv2 compatible | EPICv2 remove different design probes
if (.isEPICv2(rgSet)){
Diff_ProbeSeqA_Indices <- which(probes1$ProbeSeqA != probes2$ProbeSeqA)
commonNames <- setdiff(commonNames, probes2$Name[Diff_ProbeSeqA_Indices])
probes1 <- probes1[match(commonNames, probes1$Name), ]
probes2 <- probes2[match(commonNames, probes2$Name), ]
}
stopifnot(all(probes1$ProbeSeqA == probes2$ProbeSeqA))
# Translating rgSet2 addresses to rgSet1 addresses
translate <- probes1$AddressA
names(translate) <- probes2$AddressA
wh <- which(rownames(rgSet) %in% names(translate))
rownames(rgSet)[wh] <- translate[rownames(rgSet)[wh]]
keepAddresses$II <- unname(translate)
# Fix Bug | Save relation between rgSet2 addresses and rgSet1 addresses. Don't change rownames(rgSet) here
keepAddresses$II <- names(translate)
translate_all <- c(translate_all, translate)

# Probes of Type SnpI
probes1 <- getProbeInfo(manifest1, type = "SnpI")
probes2 <- getProbeInfo(manifest2, type = "SnpI")
commonNames <- intersect(probes1$Name, probes2$Name)
probes1 <- probes1[match(commonNames, probes1$Name),]
probes2 <- probes2[match(commonNames, probes2$Name),]
# Make EPICv2 compatible | EPICv2 remove different design probes
if (.isEPICv2(rgSet)){
Diff_ProbeSeq1A2B_Indices <- which(probes1$ProbeSeqA != probes2$ProbeSeqB)
commonNames <- setdiff(commonNames, probes2$Name[Diff_ProbeSeq1A2B_Indices])
Diff_ProbeSeq1B2A_Indices <- which(probes1$ProbeSeqB != probes2$ProbeSeqA)
commonNames <- setdiff(commonNames, probes2$Name[Diff_ProbeSeq1B2A_Indices])
probes1 <- probes1[match(commonNames, probes1$Name), ]
probes2 <- probes2[match(commonNames, probes2$Name), ]
}
stopifnot(all(probes1$ProbeSeqA == probes2$ProbeSeqB))
stopifnot(all(probes1$ProbeSeqB == probes2$ProbeSeqA))
# Translating rgSet2 addresses to rgSet1 addresses
translate <- c(probes1$AddressA, probes1$AddressB)
names(translate) <- c(probes2$AddressA, probes2$AddressB)
wh <- which(rownames(rgSet) %in% names(translate))
rownames(rgSet)[wh] <- translate[rownames(rgSet)[wh]]
keepAddresses$SnpI <- unname(translate)
# Fix Bug | Save relation between rgSet2 addresses and rgSet1 addresses. Don't change rownames(rgSet) here
keepAddresses$SnpI <- names(translate)
translate_all <- c(translate_all, translate)

# Probes of Type SnpII
probes1 <- getProbeInfo(manifest1, type = "SnpII")
Expand All @@ -103,9 +129,9 @@
# Translating rgSet2 addresses to rgSet1 addresses
translate <- probes1$AddressA
names(translate) <- probes2$AddressA
wh <- which(rownames(rgSet) %in% names(translate))
rownames(rgSet)[wh] <- translate[rownames(rgSet)[wh]]
keepAddresses$SnpII <- unname(translate)
# Fix Bug | Save relation between rgSet2 addresses and rgSet1 addresses. Don't change rownames(rgSet) here
keepAddresses$SnpII <- names(translate)
translate_all <- c(translate_all, translate)

# Probes of Type Control
probes1 <- getProbeInfo(manifest1, type = "Control")
Expand All @@ -119,6 +145,13 @@
keepAddresses <- do.call("c", keepAddresses)
keepAddresses <- keepAddresses[keepAddresses %in% rownames(rgSet)]
rgSet <- rgSet[keepAddresses, ]
# Fix Bug | Change rownames(rgSet) to rgSet1 addresses here
wh <- which(rownames(rgSet) %in% names(translate_all))
rownames(rgSet)[wh] <- translate_all[rownames(rgSet)[wh]]
# Set rownames(Green) and rownames(Red) to rgSet1 addresses
rownames(rgSet@assays@data@listData$Green) <- rownames(rgSet)
rownames(rgSet@assays@data@listData$Red) <- rownames(rgSet)
# Set annotation to outType
annotation(rgSet) <- .getAnnotationFromOutType(outType)
rgSet
}
Expand Down
4 changes: 4 additions & 0 deletions R/utils.R
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Expand Up @@ -202,6 +202,10 @@ ilogit2 <- function(x) 2^x / (1 + 2^x)
annotation(object)["array"] == "IlluminaHumanMethylationEPIC"
}

.isEPICv2 <- function(object) {
annotation(object)["array"] == "IlluminaHumanMethylationEPICv2"
}

.isAllergy <- function(object) {
annotation(object)["array"] == "IlluminaHumanMethylationAllergy"
}
Expand Down