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Compatibility with Illumina Mouse Array and EPIC Version 2 #252

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Compatibility with Illumina Mouse Array and EPIC Version 2 #252

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56 changes: 48 additions & 8 deletions R/preprocessFunnorm.R
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Original file line number Diff line number Diff line change
Expand Up @@ -209,12 +209,18 @@ preprocessFunnorm <- function(rgSet, nPCs=2, sex = NULL, bgCorr = TRUE, dyeCorr
index <- match("BISULFITE CONVERSION I", controlNames)
if (array=="IlluminaHumanMethylation450k"){
addr <- getCtrlsAddr(exType = sprintf("BS Conversion I%sC%s", c(" ", "-", "-"), 1:3), index = index)
} else if (array == "IlluminaMouseMethylation") {
ids <- paste0(rep(c(396, 140), each = 2), rep(c("U", "C"), each = 2)) # mouse BS1 ids
addr <- getCtrlsAddr(exType = sprintf("BS1-%s_MUS", ids), index = index)
} else {
addr <- getCtrlsAddr(exType = sprintf("BS Conversion I%sC%s", c("-", "-"), 1:2), index = index)
}
greenControls.current <- greenControls[[ index ]][addr,,drop=FALSE]
if (array=="IlluminaHumanMethylation450k"){
addr <- getCtrlsAddr(exType = sprintf("BS Conversion I-C%s", 4:6), index = index)
} else if (array == "IlluminaMouseMethylation"){
ids <- paste0(rep(c(409, 318, 317), each = 2), rep(c("U", "C"), each = 2)) # mouse BS1 ids
addr <- getCtrlsAddr(exType = sprintf("BS1-%s_MUS", ids), index = index)
} else {
addr <- getCtrlsAddr(exType = sprintf("BS Conversion I-C%s", 3:5), index = index)
}
Expand All @@ -228,17 +234,33 @@ preprocessFunnorm <- function(rgSet, nPCs=2, sex = NULL, bgCorr = TRUE, dyeCorr

## Staining
index <- match("STAINING", controlNames)
addr <- getCtrlsAddr(exType = "Biotin (High)", index = index)
if (array == "IlluminaMouseMethylation"){
addr <- getCtrlsAddr(exType = "STN-Biotin-High", index = index)
} else {
addr <- getCtrlsAddr(exType = "Biotin (High)", index = index)
}
stain.green <- t(greenControls[[ index ]][addr,,drop=FALSE])
addr <- getCtrlsAddr(exType = "DNP (High)", index = index)
if (array == "IlluminaMouseMethylation"){
addr <- getCtrlsAddr(exType = "STN-DNP-High", index = index)
} else {
addr <- getCtrlsAddr(exType = "DNP (High)", index = index)
}
stain.red <- t(redControls[[ index ]][addr,, drop=FALSE ])

## Extension
index <- match("EXTENSION", controlNames)
addr <- getCtrlsAddr(exType = sprintf("Extension (%s)", c("A", "T")), index = index)
if (array == "IlluminaMouseMethylation"){
addr <- getCtrlsAddr(exType = sprintf("EXT-%s", c("A", "T")), index = index)
} else {
addr <- getCtrlsAddr(exType = sprintf("Extension (%s)", c("A", "T")), index = index)
}
extension.red <- t(redControls[[index]][addr,,drop=FALSE])
colnames(extension.red) <- paste0("extRed", 1:ncol(extension.red))
addr <- getCtrlsAddr(exType = sprintf("Extension (%s)", c("C", "G")), index = index)
if (array == "IlluminaMouseMethylation"){
addr <- getCtrlsAddr(exType = sprintf("EXT-%s", c("C", "G")), index = index)
} else {
addr <- getCtrlsAddr(exType = sprintf("Extension (%s)", c("C", "G")), index = index)
}
extension.green <- t(greenControls[[index]][addr,,drop=FALSE])
colnames(extension.green) <- paste0("extGrn", 1:ncol(extension.green))

Expand All @@ -254,10 +276,18 @@ preprocessFunnorm <- function(rgSet, nPCs=2, sex = NULL, bgCorr = TRUE, dyeCorr

## Non-polymorphic probes
index <- match("NON-POLYMORPHIC", controlNames)
addr <- getCtrlsAddr(exType = sprintf("NP (%s)", c("A", "T")), index = index)
if (array == "IlluminaMouseMethylation"){
addr <- getCtrlsAddr(exType = sprintf("NPM-%s_MUS", c("A", "T")), index = index)
} else {
addr <- getCtrlsAddr(exType = sprintf("NP (%s)", c("A", "T")), index = index)
}
nonpoly.red <- t(redControls[[index]][addr, ,drop=FALSE])
colnames(nonpoly.red) <- paste0("nonpolyRed", 1:ncol(nonpoly.red))
addr <- getCtrlsAddr(exType = sprintf("NP (%s)", c("C", "G")), index = index)
if (array == "IlluminaMouseMethylation"){
addr <- getCtrlsAddr(exType = sprintf("NPM-%s_MUS", c("C", "G")), index = index)
} else {
addr <- getCtrlsAddr(exType = sprintf("NP (%s)", c("C", "G")), index = index)
}
nonpoly.green <- t(greenControls[[index]][addr, ,drop=FALSE])
colnames(nonpoly.green) <- paste0("nonpolyGrn", 1:ncol(nonpoly.green))

Expand All @@ -274,7 +304,12 @@ preprocessFunnorm <- function(rgSet, nPCs=2, sex = NULL, bgCorr = TRUE, dyeCorr

## Specificity I
index <- match("SPECIFICITY I", controlNames)
addr <- getCtrlsAddr(exType = sprintf("GT Mismatch %s (PM)", 1:3), index = index)
if(array == "IlluminaMouseMethylation"){
ids <- paste0(rep(c("PM", "MM"), 3), rep(c(1:3), each = 2))
addr <- getCtrlsAddr(exType = sprintf("SP1-%s_HSA", ids), index = index)
} else {
addr <- getCtrlsAddr(exType = sprintf("GT Mismatch %s (PM)", 1:3), index = index)
}
greenControls.current <- greenControls[[index]][addr,,drop=FALSE]
redControls.current <- redControls[[index]][addr,,drop=FALSE]
spec1.green <- t(greenControls.current)
Expand All @@ -283,7 +318,12 @@ preprocessFunnorm <- function(rgSet, nPCs=2, sex = NULL, bgCorr = TRUE, dyeCorr
colMeans2(greenControls.current, na.rm = TRUE)

index <- match("SPECIFICITY I", controlNames) # Added that line
addr <- getCtrlsAddr(exType = sprintf("GT Mismatch %s (PM)", 4:6), index = index)
if(array == "IlluminaMouseMethylation"){
ids <- paste0(rep(c("PM", "MM"), 3), rep(c(4:6), each = 2))
addr <- getCtrlsAddr(exType = sprintf("SP1-%s_HSA", ids), index = index)
} else {
addr <- getCtrlsAddr(exType = sprintf("GT Mismatch %s (PM)", 4:6), index = index)
}
greenControls.current <- greenControls[[index]][addr,,drop=FALSE]
redControls.current <- redControls[[index]][addr,,drop=FALSE]
spec1.red <- t(redControls.current)
Expand Down
28 changes: 28 additions & 0 deletions R/read.meth.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,39 @@
arrayAnnotation <- c(
array = "IlluminaHumanMethylation450k",
annotation = .default.450k.annotation)
} else if(nProbes >= 361000 && nProbes <= 362000){
arrayAnnotation <- c(
array = "IlluminaMouseMethylation",
annotation = "12.v1.mm10")

# Install package if needed
if(!require("devtools")) install.packages("devtools") # install devtools
if(!require("IlluminaMouseMethylationmanifest")) devtools::install_github("chiaraherzog/IlluminaMouseMethylationmanifest")
if(!require("IlluminaMouseMethylationanno.12.v1.mm10")) devtools::install_github("chiaraherzog/IlluminaMouseMethylationanno.12.v1.mm10")

# Load library
suppressPackageStartupMessages(library(IlluminaMouseMethylationmanifest))
suppressPackageStartupMessages(library(IlluminaMouseMethylationanno.12.v1.mm10))

} else if (nProbes >= 1050000 && nProbes <= 1053000) {
# NOTE: "Current EPIC scan type"
arrayAnnotation <- c(
array = "IlluminaHumanMethylationEPIC",
annotation = .default.epic.annotation)
} else if(nProbes >= 1104000 && nProbes <= 1110000){
arrayAnnotation <- c(
array = "IlluminaHumanMethylationEPICv2",
annotation = "20a1.hg38")

# Install package if needed
if(!require("devtools")) install.packages("devtools") # install devtools
if(!require("IlluminaHumanMethylationEPICv2manifest")) devtools::install_github("jokergoo/IlluminaHumanMethylationEPICv2manifest")
if(!require("IlluminaHumanMethylationEPICv2anno.20a1.hg38")) devtools::install_github("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")

# Load library
suppressPackageStartupMessages(library(IlluminaHumanMethylationEPICv2manifest))
suppressPackageStartupMessages(library(IlluminaHumanMethylationEPICv2anno.20a1.hg38))

} else if (nProbes >= 1032000 && nProbes <= 1033000) {
# NOTE: "Old EPIC scan type"
arrayAnnotation <- c(
Expand Down