R/probesMouse.R
In epigen/RnBeadsAnnotationCreator: RnBeads annotation creator
Defines functions
rnb.update.controlsMOUSE.enrich
rnb.update.probeMOUSE.annotation
########################################################################################################################
## probesMOUSE.R
## created: 2015-11-06
## creator: Yassen Assenov
## ---------------------------------------------------------------------------------------------------------------------
## Initializes the Infinium MethylationMOUSE probe definition tables by loading them from the Illumina website.
########################################################################################################################
## F U N C T I O N S ###################################################################################################
#' rnb.update.probeMOUSE.annotation
#'
#' Creates probe annotation tables for MethylationMOUSE.
#'
#' @param table.columns Expected columns in the probe annotation table, given as a named \code{character} vector.
#' @return \code{list} of two items:
#' \describe{
#' \item{\code{"probes"}}{\code{GRangesList} instance containing probe annotations, one \code{GRanges} per
#' chromosome.}
#' \item{\code{"controls"}}{\code{data.frame} with control probe annotation.}
#' \item{\code{"flagged"}}{\code{GRangesList} with MFG change flagged probes.}
#' }
#' @author Maximilian Schoenung
#' @noRd
rnb.update.probeMOUSE.annotation <- function(table.columns) {
#man.file <- "https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/mouse-methylation/Infinium%20Mouse%20Methylation%20v1.0%20A1%20GS%20Manifest%20File.csv"
man.file<-"https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/mouse-methylation/infinium-mouse-methylation-manifest-file-csv.zip"
## create temporary directory
dir.mouse <- file.path(.globals[['DIR.PACKAGE']], "temp", "MOUSE")
if (file.exists(dir.mouse)) {
if (unlink(dir.mouse, TRUE, TRUE) != 0) {
logger.error(c("Could not remove existing temporary directory", dir.mouse))
}
}
if (!dir.create(dir.mouse, FALSE,recursive = T)) {
logger.error(c("Could not create temporary directory", dir.mouse))
}
## Download probe definition table from Illumina's web site
destfile.zip <- file.path(dir.mouse, "probeMOUSE.csv.zip")
if (file.exists(destfile.zip)) {
logger.status(c("File", destfile.zip, "already downloaded"))
} else {
if (download.file(man.file, destfile.zip, quiet = TRUE, mode = "wb") != 0) {
logger.error(c("Could not download", man.file))
}
logger.status(c("Downloaded", man.file))
}
## Assign destfile to result
result <- unzip(zipfile=destfile.zip, exdir=dir.mouse)[1]
## Identify methylation and control probe annotation tables
txt <- scan(result, what = character(), sep = "\n", quiet = TRUE)
assay.start <- grep("^\\[Assay\\]", txt)
assay.start <- ifelse(length(assay.start) != 0, assay.start[1], 0L)
controls.start <- grep("^\\[Controls\\]", txt)
if (!(length(controls.start) == 1 && controls.start > assay.start + 1)) {
logger.error("Missing or invalid [Controls] section")
}
rm(txt); invisible(gc())
## Load the methylation and control probe annotation tables
probe.infos <- read.csv(result, skip = assay.start, nrows = controls.start - assay.start - 2, check.names = FALSE,
stringsAsFactors = FALSE)
#probe.infos2=probe.infos
probe.infos <- probe.infos[, sapply(probe.infos, function(x) { !all(is.na(x)) })]
#remove currently unused columns
probe.infos$Col<-probe.infos$Probe_Type<-probe.infos$Rep_Num<-probe.infos$Species<-NULL
if (!identical(colnames(probe.infos), names(table.columns))) {
logger.error("Unexpected columns in the probe definition table")
}
colnames(probe.infos) <- table.columns[colnames(probe.infos)]
control.probe.infos <- read.csv(result, header = FALSE, skip = controls.start, stringsAsFactors = FALSE)
control.probe.infos <- control.probe.infos[, sapply(control.probe.infos, function(x) { !all(is.na(x)) })]
logger.status("Loaded the probe definition tables from Illumina's web site")
## Validate probe.infos columns and some of the values
probe.infos[, "Design"] <- as.factor(probe.infos[, "Design"])
probe.infos[, "Color"] <- as.factor(probe.infos[, "Color"])
levels(probe.infos[, "Color"]) <- c("Both", "Grn", "Red")
probe.infos[, "Next Base"] <- as.factor(probe.infos[, "Next Base"])
probe.infos[, "Chromosome"] <- paste0("chr",probe.infos[, "Chromosome"])
probe.infos[, "Chromosome"] <- factor(as.character(probe.infos[, "Chromosome"]),
levels=paste0("chr",c(0,1:19,"MT","X","Y")))
probe.infos[, "Strand"] <- factor(probe.infos[, "Strand"],
labels=c("*","+","-"))
probe.infos[,"Context"] <- factor(toupper(substr(probe.infos[,"Name"], start = 1, stop = 2)))
control.probe.infos$V5<-NULL ### TODO: understand the meaning of the fifth column
## Validate the control probes
if (ncol(control.probe.infos) != 4) {
logger.error("Unexpected number of columns in the control probe definition table")
}
colnames(control.probe.infos) <- Mouse.CONTROL.PROBE.TABLE.COLUMNS
if (anyDuplicated(control.probe.infos$ID) != 0) {
logger.error("Duplicated IDs in the control probe definition table")
}
if (!identical(sort(unique(control.probe.infos[, 2])), unname(RnBeads:::EPIC.CONTROL.TARGETS))) {
logger.error("Unexpected values for Target in the control probe definition table")
}
control.probe.infos[, 2] <- factor(control.probe.infos[, 2], levels = unname(RnBeads:::EPIC.CONTROL.TARGETS))
control.probe.infos[, 3] <- factor(RnBeads:::capitalize(tolower(control.probe.infos[, 3])))
#control.probe.infos[, 5] <- control.probe.infos[, 5] == "AVG"
control.probe.infos <- rnb.update.controlsMOUSE.enrich(control.probe.infos)
logger.status("Processed control probe annotation table")
## Add information about CpG counts and GC content in the neighborhood, context, overlaps with SNPs
#probe.infos[, "CGI Relation"] <- NA
for(con in c("N Shelf","N Shore","CpG Island","S Shelf","S Shore")){
probe.infos[,con][probe.infos[, con]==""] <- NA
}
probes.shaped <- probe.infos[,c("Name","Chromosome","Location","Strand","Design","CpG Island","N Shelf","N Shore","S Shelf","S Shore",
"AddressA","AddressB","Color","MFG Change Flagged","ID","Context")]
probes.flagged <- probes.shaped[probes.shaped[,"MFG Change Flagged"]==TRUE,]
#probes.flagged$Chromosome<-factor(as.character(probes.flagged$Chromosome), levels=setdiff(levels(probes.flagged$Chromosome), "chr0"))
probes.shaped <- probes.shaped[probes.shaped[,"MFG Change Flagged"]==FALSE,]
probes.shaped$Chromosome<-factor(as.character(probes.shaped$Chromosome), levels=setdiff(levels(probes.shaped$Chromosome), "chr0"))
probes.shaped <- rnb.update.probe.annotation.snps(probes.shaped)
# sort and GRanges List
probes.ranges <- GenomicRanges::makeGRangesFromDataFrame(df = probes.shaped,
keep.extra.columns = T,
seqnames.field = "Chromosome",
start.field = "Location",
end.field = "Location",
strand.field = "Strand"
)
#probes.ranges <- IRanges::resize(probes.ranges,2)
width(probes.ranges) <- width(probes.ranges)+1
gr <- sort(probes.ranges, ignore.strand=TRUE)
names(gr) <- gr$ID
probes.gr <- GenomicRanges::split(gr, seqnames(gr))
probes.gr <- probes.gr[names(.globals[['CHROMOSOMES']])]
# sort and GRanges List for flagged
flagged.ranges <- GenomicRanges::makeGRangesFromDataFrame(df = probes.flagged,
keep.extra.columns = T,
seqnames.field = "Chromosome",
start.field = "Location",
end.field = "Location",
strand.field = "Strand"
)
width(flagged.ranges) <- width(flagged.ranges)+1
fl <- sort(flagged.ranges)
names(fl) <- fl$ID
probes.fl <- GenomicRanges::split(fl, seqnames(fl))
return(list(probes = probes.gr, controls = control.probe.infos, flagged=probes.fl))
}
########################################################################################################################
#' rnb.update.controlsMOUSE.enrich
#'
#' Extends the given table of control probe annotations by adding (or replacing) four columns and filling them with
#' values depending on the values of some of the original columns.
#'
#' @param control.probe.infos Table of control probe annotation in the form of a \code{data.frame} containing at least
#' the following columns: \code{"Target"}, \code{"Color"} and \code{"Description"}.
#' @return Enriched probe annotation; the given \code{data.frame} with four added or replaced columns:
#' \code{"Evaluate Green"}, \code{"Evaluate Red"}, \code{"Expected Intensity"} and \code{"Sample-dependent"}.
#' @author Pavlo Lutsik
#' @noRd
rnb.update.controlsMOUSE.enrich <- function(control.probe.infos) {
## Control probe colors associated with the evaluation of the Red channel
CONTROL.DES.GREEN <- c("ctl-BISULFITE-CONVERSION-I-140U_MUS","ctl-BISULFITE-CONVERSION-I-140M_MUS",
"ctl-BISULFITE-CONVERSION-I-303U_MUS","ctl-BISULFITE-CONVERSION-I-303M_MUS",
"ctl-BISULFITE-CONVERSION-I-2U_HSA","ctl-BISULFITE-CONVERSION-I-2M_HSA",
"ctl-BISULFITE-CONVERSION-I-3U_HSA","ctl-BISULFITE-CONVERSION-I-3M_HSA",
"ctl-EXTENSION-Extension-C","ctl-EXTENSION-Extension-G",
"ctl-NON-POLYMORPHIC-NP-C_MUS","ctl-NON-POLYMORPHIC-NP-C_HSA",
"ctl-NON-POLYMORPHIC-NP-G_MUS","ctl-NON-POLYMORPHIC-NP-G_HSA",
"ctl-RESTORATION-Restore","ctl-SPECIFICITY-I-37","ctl-SPECIFICITY-I-39",
"ctl-SPECIFICITY-I-GT-Mismatch-2-MM","ctl-SPECIFICITY-I-GT-Mismatch-2-PM"
)
## Control probe colors associated with the evaluation of the Red channel
CONTROL.DES.RED <- c("ctl-BISULFITE-CONVERSION-I-317U_MUS","ctl-BISULFITE-CONVERSION-I-317M_MUS",
"ctl-BISULFITE-CONVERSION-I-318U_MUS","ctl-BISULFITE-CONVERSION-I-318M_MUS",
"ctl-BISULFITE-CONVERSION-I-330U_MUS","ctl-BISULFITE-CONVERSION-I-330M_MUS",
"ctl-BISULFITE-CONVERSION-I-4U_HSA","ctl-BISULFITE-CONVERSION-I-4M_HSA",
"ctl-BISULFITE-CONVERSION-I-5U_HSA","ctl-BISULFITE-CONVERSION-I-5M_HSA",
"ctl-BISULFITE-CONVERSION-I-6U_HSA","ctl-BISULFITE-CONVERSION-I-6M_HSA",
"ctl-EXTENSION-Extension-A","ctl-EXTENSION-Extension-T",
"ctl-NON-POLYMORPHIC-NP-T_MUS","ctl-NON-POLYMORPHIC-NP-T_HSA",
"ctl-NON-POLYMORPHIC-NP-A_MUS","ctl-NON-POLYMORPHIC-NP-A_HSA",
"ctl-SPECIFICITY-I-34",
"ctl-SPECIFICITY-I-GT-Mismatch-4-MM","ctl-SPECIFICITY-I-GT-Mismatch-4-PM",
"ctl-SPECIFICITY-I-GT-Mismatch-5-MM","ctl-SPECIFICITY-I-GT-Mismatch-5-PM"
)
## Add columns Evaluate Green and Evaluate Red
control.probe.infos[["Evaluate Green"]] <- "-"
control.probe.infos[["Evaluate Red"]] <- "-"
i <- grep("DNP", control.probe.infos[, "Description"])
control.probe.infos[i, "Evaluate Green"] <- "-"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("Biotin", control.probe.infos[, "Description"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- (control.probe.infos[["Description"]] %in% CONTROL.DES.GREEN)
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- (control.probe.infos[["Description"]] %in% CONTROL.DES.RED)
control.probe.infos[i, "Evaluate Green"] <- "-"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("BISULFITE-CONVERSION-II",control.probe.infos[["Description"]])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("NEGATIVE", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("HYBRIDIZATION", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- grep("NORM_A", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "-"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("NORM_T", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "-"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("NORM_C", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- grep("NORM_G", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- grep("SPECIFICITY II", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("TARGET REMOVAL", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "+"
control.probe.infos[["Evaluate Green"]] <- factor(control.probe.infos[["Evaluate Green"]], levels = c("-", "+"))
control.probe.infos[["Evaluate Red"]] <- factor(control.probe.infos[["Evaluate Red"]], levels = c("-", "+"))
## Add column Expected Intensity
control.probe.infos[["Expected Intensity"]] <- as.character(NA)
i <- control.probe.infos[, "Target"] %in% c("NEGATIVE", "RESTORATION")
control.probe.infos[i, "Expected Intensity"] <- "Background"
i <- control.probe.infos[, "Target"] %in% c("TARGET REMOVAL")
control.probe.infos[i, "Expected Intensity"] <- "Low"
i <- grep("U_", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Background"
i <- grep("M_", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- c("BISULFITE CONVERSION II", "SPECIFICITY II", "EXTENSION", "NON-POLYMORPHIC")
i <- control.probe.infos[, "Target"] %in% i
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- control.probe.infos[, "Target"] %in% paste("NORM", c("A", "C", "G", "T"), sep = "_")
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- control.probe.infos[, "Target"] %in% c("SPECIFICITY I")
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- grep("-MM", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Background"
i <- grep("Bkg", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Background"
i <- grep("High", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- grep("Medium", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Medium"
i <- grep("Low", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Low"
control.probe.infos[["Expected Intensity"]] <- factor(control.probe.infos[["Expected Intensity"]])
## Add column Sample-dependent
control.probe.infos[["Sample-dependent"]] <-
!(control.probe.infos[["Target"]] %in% RnBeads:::CONTROL.TARGETS.SAMPLE.INDEPENDENT)
## Add column Index
control.probe.infos[["Index"]][order(control.probe.infos$Target)] <-
unlist(sapply(sort(unique(control.probe.infos$Target)), function(target) {
1:length(which(control.probe.infos$Target==target))
}
))
return(control.probe.infos)
}
epigen/RnBeadsAnnotationCreator documentation built on June 26, 2022, 4:28 p.m.
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Defines functions rnb.update.controlsMOUSE.enrich rnb.update.probeMOUSE.annotation
########################################################################################################################
## probesMOUSE.R
## created: 2015-11-06
## creator: Yassen Assenov
## ---------------------------------------------------------------------------------------------------------------------
## Initializes the Infinium MethylationMOUSE probe definition tables by loading them from the Illumina website.
########################################################################################################################
## F U N C T I O N S ###################################################################################################
#' rnb.update.probeMOUSE.annotation
#'
#' Creates probe annotation tables for MethylationMOUSE.
#'
#' @param table.columns Expected columns in the probe annotation table, given as a named \code{character} vector.
#' @return \code{list} of two items:
#' \describe{
#' \item{\code{"probes"}}{\code{GRangesList} instance containing probe annotations, one \code{GRanges} per
#' chromosome.}
#' \item{\code{"controls"}}{\code{data.frame} with control probe annotation.}
#' \item{\code{"flagged"}}{\code{GRangesList} with MFG change flagged probes.}
#' }
#' @author Maximilian Schoenung
#' @noRd
rnb.update.probeMOUSE.annotation <- function(table.columns) {
#man.file <- "https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/mouse-methylation/Infinium%20Mouse%20Methylation%20v1.0%20A1%20GS%20Manifest%20File.csv"
man.file<-"https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/mouse-methylation/infinium-mouse-methylation-manifest-file-csv.zip"
## create temporary directory
dir.mouse <- file.path(.globals[['DIR.PACKAGE']], "temp", "MOUSE")
if (file.exists(dir.mouse)) {
if (unlink(dir.mouse, TRUE, TRUE) != 0) {
logger.error(c("Could not remove existing temporary directory", dir.mouse))
}
}
if (!dir.create(dir.mouse, FALSE,recursive = T)) {
logger.error(c("Could not create temporary directory", dir.mouse))
}
## Download probe definition table from Illumina's web site
destfile.zip <- file.path(dir.mouse, "probeMOUSE.csv.zip")
if (file.exists(destfile.zip)) {
logger.status(c("File", destfile.zip, "already downloaded"))
} else {
if (download.file(man.file, destfile.zip, quiet = TRUE, mode = "wb") != 0) {
logger.error(c("Could not download", man.file))
}
logger.status(c("Downloaded", man.file))
}
## Assign destfile to result
result <- unzip(zipfile=destfile.zip, exdir=dir.mouse)[1]
## Identify methylation and control probe annotation tables
txt <- scan(result, what = character(), sep = "\n", quiet = TRUE)
assay.start <- grep("^\\[Assay\\]", txt)
assay.start <- ifelse(length(assay.start) != 0, assay.start[1], 0L)
controls.start <- grep("^\\[Controls\\]", txt)
if (!(length(controls.start) == 1 && controls.start > assay.start + 1)) {
logger.error("Missing or invalid [Controls] section")
}
rm(txt); invisible(gc())
## Load the methylation and control probe annotation tables
probe.infos <- read.csv(result, skip = assay.start, nrows = controls.start - assay.start - 2, check.names = FALSE,
stringsAsFactors = FALSE)
#probe.infos2=probe.infos
probe.infos <- probe.infos[, sapply(probe.infos, function(x) { !all(is.na(x)) })]
#remove currently unused columns
probe.infos$Col<-probe.infos$Probe_Type<-probe.infos$Rep_Num<-probe.infos$Species<-NULL
if (!identical(colnames(probe.infos), names(table.columns))) {
logger.error("Unexpected columns in the probe definition table")
}
colnames(probe.infos) <- table.columns[colnames(probe.infos)]
control.probe.infos <- read.csv(result, header = FALSE, skip = controls.start, stringsAsFactors = FALSE)
control.probe.infos <- control.probe.infos[, sapply(control.probe.infos, function(x) { !all(is.na(x)) })]
logger.status("Loaded the probe definition tables from Illumina's web site")
## Validate probe.infos columns and some of the values
probe.infos[, "Design"] <- as.factor(probe.infos[, "Design"])
probe.infos[, "Color"] <- as.factor(probe.infos[, "Color"])
levels(probe.infos[, "Color"]) <- c("Both", "Grn", "Red")
probe.infos[, "Next Base"] <- as.factor(probe.infos[, "Next Base"])
probe.infos[, "Chromosome"] <- paste0("chr",probe.infos[, "Chromosome"])
probe.infos[, "Chromosome"] <- factor(as.character(probe.infos[, "Chromosome"]),
levels=paste0("chr",c(0,1:19,"MT","X","Y")))
probe.infos[, "Strand"] <- factor(probe.infos[, "Strand"],
labels=c("*","+","-"))
probe.infos[,"Context"] <- factor(toupper(substr(probe.infos[,"Name"], start = 1, stop = 2)))
control.probe.infos$V5<-NULL ### TODO: understand the meaning of the fifth column
## Validate the control probes
if (ncol(control.probe.infos) != 4) {
logger.error("Unexpected number of columns in the control probe definition table")
}
colnames(control.probe.infos) <- Mouse.CONTROL.PROBE.TABLE.COLUMNS
if (anyDuplicated(control.probe.infos$ID) != 0) {
logger.error("Duplicated IDs in the control probe definition table")
}
if (!identical(sort(unique(control.probe.infos[, 2])), unname(RnBeads:::EPIC.CONTROL.TARGETS))) {
logger.error("Unexpected values for Target in the control probe definition table")
}
control.probe.infos[, 2] <- factor(control.probe.infos[, 2], levels = unname(RnBeads:::EPIC.CONTROL.TARGETS))
control.probe.infos[, 3] <- factor(RnBeads:::capitalize(tolower(control.probe.infos[, 3])))
#control.probe.infos[, 5] <- control.probe.infos[, 5] == "AVG"
control.probe.infos <- rnb.update.controlsMOUSE.enrich(control.probe.infos)
logger.status("Processed control probe annotation table")
## Add information about CpG counts and GC content in the neighborhood, context, overlaps with SNPs
#probe.infos[, "CGI Relation"] <- NA
for(con in c("N Shelf","N Shore","CpG Island","S Shelf","S Shore")){
probe.infos[,con][probe.infos[, con]==""] <- NA
}
probes.shaped <- probe.infos[,c("Name","Chromosome","Location","Strand","Design","CpG Island","N Shelf","N Shore","S Shelf","S Shore",
"AddressA","AddressB","Color","MFG Change Flagged","ID","Context")]
probes.flagged <- probes.shaped[probes.shaped[,"MFG Change Flagged"]==TRUE,]
#probes.flagged$Chromosome<-factor(as.character(probes.flagged$Chromosome), levels=setdiff(levels(probes.flagged$Chromosome), "chr0"))
probes.shaped <- probes.shaped[probes.shaped[,"MFG Change Flagged"]==FALSE,]
probes.shaped$Chromosome<-factor(as.character(probes.shaped$Chromosome), levels=setdiff(levels(probes.shaped$Chromosome), "chr0"))
probes.shaped <- rnb.update.probe.annotation.snps(probes.shaped)
# sort and GRanges List
probes.ranges <- GenomicRanges::makeGRangesFromDataFrame(df = probes.shaped,
keep.extra.columns = T,
seqnames.field = "Chromosome",
start.field = "Location",
end.field = "Location",
strand.field = "Strand"
)
#probes.ranges <- IRanges::resize(probes.ranges,2)
width(probes.ranges) <- width(probes.ranges)+1
gr <- sort(probes.ranges, ignore.strand=TRUE)
names(gr) <- gr$ID
probes.gr <- GenomicRanges::split(gr, seqnames(gr))
probes.gr <- probes.gr[names(.globals[['CHROMOSOMES']])]
# sort and GRanges List for flagged
flagged.ranges <- GenomicRanges::makeGRangesFromDataFrame(df = probes.flagged,
keep.extra.columns = T,
seqnames.field = "Chromosome",
start.field = "Location",
end.field = "Location",
strand.field = "Strand"
)
width(flagged.ranges) <- width(flagged.ranges)+1
fl <- sort(flagged.ranges)
names(fl) <- fl$ID
probes.fl <- GenomicRanges::split(fl, seqnames(fl))
return(list(probes = probes.gr, controls = control.probe.infos, flagged=probes.fl))
}
########################################################################################################################
#' rnb.update.controlsMOUSE.enrich
#'
#' Extends the given table of control probe annotations by adding (or replacing) four columns and filling them with
#' values depending on the values of some of the original columns.
#'
#' @param control.probe.infos Table of control probe annotation in the form of a \code{data.frame} containing at least
#' the following columns: \code{"Target"}, \code{"Color"} and \code{"Description"}.
#' @return Enriched probe annotation; the given \code{data.frame} with four added or replaced columns:
#' \code{"Evaluate Green"}, \code{"Evaluate Red"}, \code{"Expected Intensity"} and \code{"Sample-dependent"}.
#' @author Pavlo Lutsik
#' @noRd
rnb.update.controlsMOUSE.enrich <- function(control.probe.infos) {
## Control probe colors associated with the evaluation of the Red channel
CONTROL.DES.GREEN <- c("ctl-BISULFITE-CONVERSION-I-140U_MUS","ctl-BISULFITE-CONVERSION-I-140M_MUS",
"ctl-BISULFITE-CONVERSION-I-303U_MUS","ctl-BISULFITE-CONVERSION-I-303M_MUS",
"ctl-BISULFITE-CONVERSION-I-2U_HSA","ctl-BISULFITE-CONVERSION-I-2M_HSA",
"ctl-BISULFITE-CONVERSION-I-3U_HSA","ctl-BISULFITE-CONVERSION-I-3M_HSA",
"ctl-EXTENSION-Extension-C","ctl-EXTENSION-Extension-G",
"ctl-NON-POLYMORPHIC-NP-C_MUS","ctl-NON-POLYMORPHIC-NP-C_HSA",
"ctl-NON-POLYMORPHIC-NP-G_MUS","ctl-NON-POLYMORPHIC-NP-G_HSA",
"ctl-RESTORATION-Restore","ctl-SPECIFICITY-I-37","ctl-SPECIFICITY-I-39",
"ctl-SPECIFICITY-I-GT-Mismatch-2-MM","ctl-SPECIFICITY-I-GT-Mismatch-2-PM"
)
## Control probe colors associated with the evaluation of the Red channel
CONTROL.DES.RED <- c("ctl-BISULFITE-CONVERSION-I-317U_MUS","ctl-BISULFITE-CONVERSION-I-317M_MUS",
"ctl-BISULFITE-CONVERSION-I-318U_MUS","ctl-BISULFITE-CONVERSION-I-318M_MUS",
"ctl-BISULFITE-CONVERSION-I-330U_MUS","ctl-BISULFITE-CONVERSION-I-330M_MUS",
"ctl-BISULFITE-CONVERSION-I-4U_HSA","ctl-BISULFITE-CONVERSION-I-4M_HSA",
"ctl-BISULFITE-CONVERSION-I-5U_HSA","ctl-BISULFITE-CONVERSION-I-5M_HSA",
"ctl-BISULFITE-CONVERSION-I-6U_HSA","ctl-BISULFITE-CONVERSION-I-6M_HSA",
"ctl-EXTENSION-Extension-A","ctl-EXTENSION-Extension-T",
"ctl-NON-POLYMORPHIC-NP-T_MUS","ctl-NON-POLYMORPHIC-NP-T_HSA",
"ctl-NON-POLYMORPHIC-NP-A_MUS","ctl-NON-POLYMORPHIC-NP-A_HSA",
"ctl-SPECIFICITY-I-34",
"ctl-SPECIFICITY-I-GT-Mismatch-4-MM","ctl-SPECIFICITY-I-GT-Mismatch-4-PM",
"ctl-SPECIFICITY-I-GT-Mismatch-5-MM","ctl-SPECIFICITY-I-GT-Mismatch-5-PM"
)
## Add columns Evaluate Green and Evaluate Red
control.probe.infos[["Evaluate Green"]] <- "-"
control.probe.infos[["Evaluate Red"]] <- "-"
i <- grep("DNP", control.probe.infos[, "Description"])
control.probe.infos[i, "Evaluate Green"] <- "-"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("Biotin", control.probe.infos[, "Description"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- (control.probe.infos[["Description"]] %in% CONTROL.DES.GREEN)
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- (control.probe.infos[["Description"]] %in% CONTROL.DES.RED)
control.probe.infos[i, "Evaluate Green"] <- "-"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("BISULFITE-CONVERSION-II",control.probe.infos[["Description"]])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("NEGATIVE", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("HYBRIDIZATION", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- grep("NORM_A", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "-"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("NORM_T", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "-"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("NORM_C", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- grep("NORM_G", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "-"
i <- grep("SPECIFICITY II", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "+"
i <- grep("TARGET REMOVAL", control.probe.infos[, "Target"])
control.probe.infos[i, "Evaluate Green"] <- "+"
control.probe.infos[i, "Evaluate Red"] <- "+"
control.probe.infos[["Evaluate Green"]] <- factor(control.probe.infos[["Evaluate Green"]], levels = c("-", "+"))
control.probe.infos[["Evaluate Red"]] <- factor(control.probe.infos[["Evaluate Red"]], levels = c("-", "+"))
## Add column Expected Intensity
control.probe.infos[["Expected Intensity"]] <- as.character(NA)
i <- control.probe.infos[, "Target"] %in% c("NEGATIVE", "RESTORATION")
control.probe.infos[i, "Expected Intensity"] <- "Background"
i <- control.probe.infos[, "Target"] %in% c("TARGET REMOVAL")
control.probe.infos[i, "Expected Intensity"] <- "Low"
i <- grep("U_", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Background"
i <- grep("M_", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- c("BISULFITE CONVERSION II", "SPECIFICITY II", "EXTENSION", "NON-POLYMORPHIC")
i <- control.probe.infos[, "Target"] %in% i
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- control.probe.infos[, "Target"] %in% paste("NORM", c("A", "C", "G", "T"), sep = "_")
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- control.probe.infos[, "Target"] %in% c("SPECIFICITY I")
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- grep("-MM", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Background"
i <- grep("Bkg", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Background"
i <- grep("High", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "High"
i <- grep("Medium", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Medium"
i <- grep("Low", control.probe.infos[, "Description"])
control.probe.infos[i, "Expected Intensity"] <- "Low"
control.probe.infos[["Expected Intensity"]] <- factor(control.probe.infos[["Expected Intensity"]])
## Add column Sample-dependent
control.probe.infos[["Sample-dependent"]] <-
!(control.probe.infos[["Target"]] %in% RnBeads:::CONTROL.TARGETS.SAMPLE.INDEPENDENT)
## Add column Index
control.probe.infos[["Index"]][order(control.probe.infos$Target)] <-
unlist(sapply(sort(unique(control.probe.infos$Target)), function(target) {
1:length(which(control.probe.infos$Target==target))
}
))
return(control.probe.infos)
}
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