Nothing
#'
#' This function applies the PELT method to segment each signal of the dataset and launches CGHcall for calling segments and detect aberrations.
#' Results will be stored in a text file in the segmentation folder of the aroma architecture.
#'
#' @title Segment a copy-number signal and call the found segments.
#'
#' @param dataSetName name of the data-set folder in the rawData folder containing the signals to use.
#' @param normalTumorArray Only in the case of normal-tumor study. A csv file or a data.frame containing the mapping between normal and tumor files.
#' The first column contains the name of normal files and the second the names of associated tumor files.
#' @param chromosome A vector containing the chromosomes to segment.
#' @param Rho A Vector containing all the penalization values to test for the segmentation. If no values are provided, default values will be used.
#' @param listOfFiles A vector containing the names of the files from the dataSetName to use.
#' @param onlySNP If TRUE, only the SNP probes will be used.
#' @param savePlot If TRUE, save the segmented signal in figures folder.
#' @param nclass The number of levels to be used for calling. Either 3 (loss, normal, gain), 4 (including amplifications), 5 (including double deletions) (default=3).
#' @param cellularity Percentage of tumored cells in the sample (default=1).
#' @param ... Other parameters of CGHcall function
#'
#' @return a data.frame containg columns :
#' \describe{
#' \item{sampleNames}{Name of the file.}
#' \item{chrom}{The chromosome of the segment.}
#' \item{chromStart}{The starting position (in bp) of a segment. This position is not included in the segment.}
#' \item{chromEnd}{The ending position (in bp) of a segment.This position is included in the segment.}
#' \item{probes}{Number of probes in the segment.}
#' \item{means}{Mean of the segment.}
#' \item{calls}{The calling of segment ("double loss", "loss", "normal", "gain" or "amplification").}
#' }
#'
#' @examples
#' \dontrun{
#' #DO NOT EXECUTE before reading the vignette
#' seg1=cnSegCallingProcess("data1",normalTumorArray,chromosome=20:21)
#' seg2=cnSegCallingProcess("data2",chromosome=20:21)
#' }
#'
#' @export
#'
#' @author Quentin Grimonprez
#'
cnSegCallingProcess=function(dataSetName,normalTumorArray,chromosome=1:22,Rho=NULL,listOfFiles=NULL,onlySNP=TRUE,savePlot=TRUE,nclass=3,cellularity=1,...)
{
requireNamespace("R.devices")
allpkg=TRUE
if(!suppressPackageStartupMessages(requireNamespace("aroma.affymetrix", quietly=TRUE) ) )
{
message("Package not found: aroma.affymetrix. For download it:\n")
message("source(\"http://callr.org/install#HenrikBengtsson/sfit\")\n")
message("if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n")
message("install.packages(\"BiocManager\")\n")
message("BiocManager::install(\"affxparser\")\n")
message("BiocManager::install(\"DNAcopy\")\n")
message("BiocManager::install(\"aroma.light\")\n")
message("install.packages(\"aroma.affymetrix\")\n")
allpkg=FALSE
}
# else
# message("Package aroma.affymetrix loaded.\n")
if(!suppressPackageStartupMessages(requireNamespace("aroma.cn", quietly=TRUE) ) )
{
message("Package not found: aroma.cn. For download it:\n")
message("install.packages(\"aroma.cn\")\n")
allpkg=FALSE
}
if(!allpkg)
stop("You have to install some packages : Follow the printed informations.")
requireNamespace("aroma.core")
requireNamespace("R.filesets")
if(!("totalAndFracBData"%in%list.files()))
stop("There is no \"totalAndFracBData\", check if you are in the good working directory or if you have run the signalPreProcess function before.")
###check the arguments
#dataSetName
if(missing(dataSetName))
stop("dataSetName is missing.")
if(!is.character(dataSetName))
stop("dataSetName must be the name of a folder in \"rawData\" folder.")
if(!(dataSetName%in%list.files("rawData")))
stop("dataSetName must be the name of a folder in \"rawData\" folder.")
#onlySNP
if(!is.logical(onlySNP))
stop("onlyDNP must be a boolean.")
#check if we are in a normal-tumor study or in a single array study
singleStudy=TRUE
if(!missing(normalTumorArray))
singleStudy=FALSE
#################### import the dataSet to have the name of all the files
#path where find the CN data
rootPath <- "totalAndFracBData";
rootPath <- Arguments$getReadablePath(rootPath);
dataSet <- paste0(dataSetName,",ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY");
#load CN
dsC <- aroma.core::AromaUnitTotalCnBinarySet$byName(dataSet, chipType="*", paths=rootPath);
################### check normalTumorArray
if(!singleStudy)
{
#normalTumorArray
if(is.character(normalTumorArray))
normalTumorArray=read.csv(normalTumorArray)
else
{
if(!is.data.frame(normalTumorArray))
stop("normalTumorArray must be either the path to the normalTumorArray csv file or a data.frame containing the data.\n")
}
#check normalTumorArray
if(!("normal"%in%colnames(normalTumorArray)) || !("tumor"%in%colnames(normalTumorArray)))
stop("normalTumorArray doesn't contain a column \"normal\" or \"tumor\".\n")
# isArrayComplete=sapply(R.filesets::getNames(dsC),FUN=function(name,listOfNames){name%in%listOfNames},c(as.character(normalTumorArray$normal),as.character(normalTumorArray$tumor)))
# if(sum(isArrayComplete)!=length(isArrayComplete))
# stop("normalTumorArray doesn't contain all the filenames of dataSetName.")
}
###### check listOfFiles
pos=c()
if(is.null(listOfFiles) || missing(listOfFiles))
{
listOfFiles=R.filesets::getNames(dsC)
pos=1:length(dsC)
}
else
{
#check the format
if(!is.vector(listOfFiles) || !is.character(listOfFiles))
stop("listOfFiles must be a vector of string.")
listOfFiles=unique(listOfFiles)
#check if all the files of listOfFiles are in the folder
pos=sapply(listOfFiles,match,R.filesets::getNames(dsC))#position of the files of listOfFiles in the folder
if(length(which(pos>0))!=length(pos))
stop("Wrong name of files in listOfFiles")
}
if(!singleStudy)
{
isArrayComplete=sapply(listOfFiles,FUN=function(name,listOfNames){name%in%listOfNames},c(as.character(normalTumorArray$normal),as.character(normalTumorArray$tumor)))
if(sum(isArrayComplete)!=length(isArrayComplete))
stop("normalTumorArray doesn't contain all the filenames you specified in listOfFiles parameter.")
}
#if single array study, we just reduce dsC to pos
if(!singleStudy)
{
#if normal-tumor study, we need the tumor and normal files
#we obtain the complementary files
compFiles=getComplementaryFile(listOfFiles,normalTumorArray)
allFiles=unique(c(listOfFiles,compFiles))
#index of the files
pos=sapply(allFiles,FUN=function(x,dsC){which(R.filesets::getNames(dsC)==x)},dsC)
tag=getStatus(allFiles,normalTumorArray)
pos=pos[which(tag=="tumor")]
}
#Rho
if(missing(Rho) || is.null(Rho))
Rho=c(seq(0.1,2,by=0.1),seq(2.2,5,by=0.2),seq(5.5,10,by=0.2),seq(11,16,by=1),seq(18,36,by=2),seq(40,80,by=4))
######################### END CHECK PARAMETERS
figPath <- Arguments$getWritablePath(paste0("figures/",dataSetName,"/segmentation/CN/"));
#names of the files to segment
names=R.filesets::getNames(dsC)[pos]
output=lapply(names,FUN=function(name)
{
cghArg=list()
segmentList=data.frame()
for(chr in chromosome)
{
#get the copy-number for 1 chr
if(!singleStudy)
CN=getCopyNumberSignal(dataSetName,chr,normalTumorArray,onlySNP,name,verbose=FALSE)
else
CN=getCopyNumberSignal(dataSetName,chr,onlySNP=onlySNP,listOfFiles=name,verbose=FALSE)
CN=CN[[paste0("chr",chr)]]
gc()
#segmentation
if (length(which(!is.na(as.vector(CN[,3]))))<2)
{
if (chr==24)
{
message(paste0("Cannot segment file ",name," chromosome Y (24) : gender = XX\n"))
} else {
message(paste0("Cannot segment file ",name," chromosome ",chr, ": less than 2 points in the signal\n"))
}
} else {
message(paste0("Segmentation of file ",name," chromosome ",chr,"..."))
seg=PELT(as.vector(CN[,3]),Rho,CN$position,plot=TRUE,verbose=FALSE)
message("OK\n")
if(savePlot)
{
figName <- sprintf("%s,%s", name, chr);
pathname <- filePath(figPath, sprintf("%s.png", figName));
width <- 1280;
aspect <- 0.6*1/3;
fig <- R.devices::devNew("png", pathname, label=figName, width=width, height=2*aspect*width);
plot(NA,xlim=c(min(CN$position),max(CN$position)), ylim=c(0,6),xlab="Position", main=figName,ylab="CN", pch=".")
points(CN$position, CN[,3], pch=".");
for(i in 1:nrow(seg$segment))
lines(c(seg$segment$start[i],seg$segment$end[i]),rep(seg$segment$means[i],2),col="red",lwd=3)
R.devices::devDone();
}
#concatenate the results
cghArg=list(copynumber=rbind(cghArg$copynumber,seg$signal),
segmented=rbind(cghArg$segmented,seg$segmented),
startPos=c(cghArg$startPos,CN$position),
chromosome=c(cghArg$chromosome,CN$chromosome),
sampleNames=name,
featureNames=c(cghArg$featureNames,CN$featureNames))
#output for the bed file
segmentList=data.frame(chrom=c(as.character(segmentList$chrom),rep(paste0("chr",CN$chromosome[1]),length(seg$segment$start))),
chromStart=c(segmentList$chromStart,seg$segment$start),
chromEnd=c(segmentList$chromEnd,seg$segment$end),
probes=c(segmentList$probes,seg$segment$points),
means=c(segmentList$means,seg$segment$means))
}
}
if (length(cghArg)>0)
{
#launch calling process
cghArg=callingProcess(cghArg,nclass=nclass,cellularity=cellularity,verbose=FALSE,...)
#get the calling for each segment
calls=apply(segmentList,1,FUN=function(segment)
{
#we restrict to the chromosome of the segment
indChr=which(cghArg$chromosome==as.numeric(substr(as.character(segment[1]),4,nchar(as.character(segment[1])))))
#we search the starting position of the segment
indPos=which(cghArg$startPos[indChr]==(as.numeric(segment[2])))[1]
#print(indPos)
# calling of the start of the segment=calling of the segment
return(cghArg$calls[indChr[indPos]])
})
###bed files output
#results are stored in the segmentation folder
#check the existence of the segmentation folder
if(!("segmentation"%in%list.files()))
dir.create("segmentation");
#check the existence of th dataSet folder in segmentation folder
if(!(dataSetName%in%list.files("segmentation")))
dir.create(paste0("segmentation/",dataSetName));
if(!("CN"%in%list.files(paste0("segmentation/",dataSetName))))
dir.create(paste0("segmentation/",dataSetName,"/CN"));
#output=segment+calls
output=data.frame(segmentList,calls=calls)
#write in .bed
write.table(output,file=paste0("segmentation/",dataSetName,"/CN/",name,",calls.bed"),sep="\t",row.names=FALSE)
return(data.frame(sampleNames=rep(name,nrow(output)),output))
}
})
return(do.call(rbind,output))
}
##########################################################################################################################################
#'
#' This function filters the output of a segmentation and label process.
#' It allows to keep only segments over a minimal length or containing at least a minimal number of probes.
#'
#' @title Filter segments
#'
#' @param segmentList A data.frame containing a description of segments, it must have at least columns named "chromStart", "chromEnd", "probes" and "calls".
#' (see the output of \link{cnSegCallingProcess} function).
#' @param minLength The minimum length (in bp) for a segment. All the shorter segments are removed.
#' @param minProbes The minimum number of probes for a segment. All the segments with less probes are removed.
#' @param keptLabel Vector of labels to keep. Only segment with one of the specified label will be kept.
#'
#' @return a data.frame of the same format as segmentList.
#'
#' @export
#'
#' @author Quentin Grimonprez
#'
filterSeg=function(segmentList,minLength=1,minProbes=1,keptLabel=c("loss","gain"))
{
########check parameters
#segmentList
if(missing(segmentList))
stop("segmentList is missing.")
if(!is.data.frame(segmentList))
stop("segmentList must be a data.frame.")
if(!("calls"%in%names(segmentList)))
stop("The column \"calls\" from segmentList is missing.")
if(!("probes"%in%names(segmentList)))
stop("The column \"probes\" from segmentList is missing.")
if(!("chromStart"%in%names(segmentList)))
stop("The column \"chromStart\" from segmentList is missing.")
if(!("chromEnd"%in%names(segmentList)))
stop("The column \"chromEnd\" from segmentList is missing.")
#minLength
if(!is.numeric(minLength))
stop("minLength must be a positive integer.")
if(minLength<0)
stop("minLength must be a positive integer.")
if(!is.wholenumber(minLength))
stop("minLength must be a positive integer.")
#minProbes
if(!is.numeric(minProbes))
stop("minProbes must be a positive integer.")
if(minProbes<0)
stop("minProbes must be a positive integer.")
if(!is.wholenumber(minProbes))
stop("minProbes must be a positive integer.")
#keptLabel
if(!is.character(keptLabel) || !is.vector(keptLabel))
stop("keptLabel must be a vector of chracter.")
#########
#keep only segments with the specified label
ind=c()
for(label in keptLabel)
ind=c(ind,which(segmentList$calls==label))
segmentList=segmentList[ind,]
#remove the segments shorter than minLength pb
segmentList=segmentList[segmentList$chromEnd-segmentList$chromStart>=minLength,]
#remove the segments containing not enough probes
segmentList=segmentList[segmentList$probes>=minProbes,]
return(segmentList)
}
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