Nothing
R/parseMAGE.r
In ArrayExpress: Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Defines functions
cleanupAE
getSDRFcolumn
preparePhenoDataFor2channel
getDataColsForAE1
getDataFormat
getPhenoDataPerAD
skipADFheader
readExperimentData
readFeatures
readAEdata
readPhenoData
isOneChannel
# TODO: Add comment
#
# Author: iemam
###############################################################################
headers<-list(
ae1=c("metaColumn","metaRow","row","column"),
genepix=c("Block","Column","Row","X","Y"),
arrayvision=c("Primary","Secondary"),
agilent=c("Row","Col","PositionX","PositionY"),
scanalyze=c("GRID","COL","ROW","LEFT","TOP","RIGHT","BOT"),
scanarray=c('Array Column','Array Row','Spot Column','Spot Row','X','Y'),
quantarray=c('Array Column', 'Array Row', 'Column', 'Row'),
spotfinder=c("MC","MR","SC","SR","C","R"),
mev=c("MC","MR","C","R","UID"),
codelink=c("Logical_row","Logical_col","Center_X","Center_Y"),
bluefuse=c("COL","ROW","SUBGRIDCOL","SUBGRIDROW"),
UCSFSpot=c("Arr-colx","Arr-rowy","Spot-colx","Spot-rowy"),
NimbleScanFeature=c("X","Y","PROBE_ID","X_PIXEL","Y_PIXEL"),
NimblegenNASA=c("X_BC","Y_BC","Feature_ID","ProbID_BC"),
imagene=c('Meta Column', 'Meta Row', 'Column', 'Row', 'Field', 'Gene ID'),
ImaGene3=c("Meta_col","Meta_row","Sub_col","Sub_row","Name","Selected"),
ImaGene7=c("Block","Column","Row","Ch1 XCoord","Ch1 YCoord", "Ch2 XCoord", "Ch2 YCoord"),
ImaGeneFields=c("Field","Column","Row","XCoord","YCoord"),
CSIRO_Spot=c("grid_c","grid_r","spot_c","spot_r","indexs")
#add illumina
)
isOneChannel = function(sdrf,path){
ph = try(read.AnnotatedDataFrame(sdrf, path = path, row.names = NULL, blank.lines.skip = TRUE, fill = TRUE, varMetadata.char = "$", quote="\""))
labelCol = getSDRFcolumn("label",varLabels(ph))
if(length(labelCol)==0)
return(TRUE) # assume 1-color if no label reported - we warn the user in readPhenoData
else
return(length(unique(tolower(ph[[labelCol]])))==1)
}
readPhenoData = function(sdrf,path){
message("ArrayExpress: Reading pheno data from SDRF")
ph = try(read.AnnotatedDataFrame(sdrf, path = path, row.names = NULL, blank.lines.skip = TRUE, fill = TRUE, varMetadata.char = "$", quote="\""))
arrayDataCol = getSDRFcolumn("ArrayDataFile",varLabels(ph))
labelCol = getSDRFcolumn("label",varLabels(ph))
if(length(arrayDataCol)==0)
warning("ArrayExpress: Cannot find 'Array Data File' column in SDRF. Object might not be created correctly.")
if(length(labelCol)==0)
warning("ArrayExpress: Cannot find 'Label' column in SDRF. Object might not be created correctly.")
ph = ph[gsub(" ", "", ph$Array.Data.File) != ""]
sampleNames(ph) = ph$Array.Data.File
ph@varMetadata['Array.Data.File','labelDescription'] = "Index"
ph@varMetadata['Array.Data.File','channel'] = as.factor("_ALL_")
#Remove empty rows from pheno data
emptylines = which(sapply(seq_len(nrow(pData(ph))), function(i) all(pData(ph)[i,] == "",na.rm = TRUE)))
if(length(emptylines) != 0)
pData(ph) = pData(ph)[-emptylines,]
phenoData = pData(ph)
if(length(arrayDataCol)!=0 && length(labelCol)!=0){
#filter out duplicated rows where multiple derived data files are available per one array data file
ph=ph[!duplicated(phenoData[,c(arrayDataCol,labelCol)])]
}
#treat SDRF for two channel experiments
if(length(labelCol)==1 && length(unique(tolower(ph[[labelCol]])))==2){
arrayFilesNum = length(unique(ph[[arrayDataCol]]))
si = pData(ph)[1:(arrayFilesNum*2),]
lab = split(si,si[,"Label"])
if(nrow(lab[[1]]) != nrow(lab[[2]])){
stop("Number of CY3/CY5 is not equal")
}
#Reorder rows in each group (Cy3,Cy5) to the same order
lab[[1]] = lab[[1]][order(lab[[1]][,arrayDataCol]),]
lab[[2]] = lab[[2]][order(lab[[2]][,arrayDataCol]),]
same = which(lapply(1:ncol(lab[[1]]), function(i) all(lab[[1]][i] == lab[[2]][i])) == TRUE)
all = lab[[1]][same]
gspe = lab[[1]][-same]
colnames(gspe) = paste(colnames(gspe),names(lab)[1],sep = ".")
rspe = lab[[2]][-same]
colnames(rspe) = paste(colnames(rspe),names(lab)[2],sep = ".")
metaData = data.frame(labelDescription = c(rep("_ALL_",ncol(all)),rep("G",ncol(gspe)),rep("R",ncol(rspe))))
ph = new("AnnotatedDataFrame", data = cbind(all,gspe,rspe), varMetadata = metaData)
arrayDataCol = getSDRFcolumn("ArrayDataFile",varLabels(ph))
rownames(pData(ph)) = gsub(".[a-z][a-z][a-z]$","",ph[[arrayDataCol]],ignore.case=T)
}
# if(!all(basename(files) %in% pData(ph)[,getSDRFcolumn("ArrayDataFile",varLabels(ph))]))
# warning("Some data files in the zip archive are missing from the SDRF. The object may not be built.")
return(ph)
}
readAEdata = function(path,files,dataCols,green.only){
message("ArrayExpress: Reading data files")
source = getDataFormat(path,files)
#process extra arguments passed to read.maimages
# if (!is.null(dataCols)) {
# if (length(rawcol) > 1 && !is(rawcol, "list"))
# stop("The argument 'rawcol' must be a list if multiple column name are given.")
# if (length(rawcol) == 1 && !is(rawcol, "character"))
# stop("The argument 'rawcol' must be a character if one column name is given.")
# if (is(rawcol, "list") && !("R" %in% names(rawcol) && "G" %in% names(rawcol)))
# stop("The names of the columns must contain R and G.")
# }
if(source == "affy"){
rawdata = try(oligo::read.celfiles(filenames = file.path(path,unique(files))))
if(inherits(rawdata, 'try-error')){
stop("Unable to read cel files in",path)
}
return(rawdata)
}else if(source=="ae1"){
#Old AE1 formatted data files
if (is.null(dataCols)){
dataCols= try(getDataColsForAE1(path,files))
if(inherits(dataCols,'try-error')) return()
}
rawdata = try(read.maimages(files=files,path=path,source="generic",columns=dataCols,annotation=headers$ae1))
if(!inherits(rawdata, 'try-error')) rawdata$source="ae1"
}else if(source %in% c("agilent","arrayvision","bluefuse","genepix","bluefuse","imagene","quantarray")){
#data format can be directly read by limma
rawdata = try(read.maimages(files=files,path=path,source=source,columns=dataCols,green.only=green.only))
}else if(!is.null(dataCols) && source=="unknown"){
#read generic source given columns specified by user
rawdata = try(read.maimages(files=files,path=path,source="generic",columns=dataCols,green.only=green.only))
}else
# TODO: add more formats (illumina)
stop("Unable to recognize data file format")
if(inherits(rawdata, 'try-error')){
stop("Unable to read data files in",path)
}
#reorder rows of RGList to reflect the same order in ADF as Block Row/Block Column/Row/Column
if(is.null(rawdata$genes))
stop("Unable to read probe annotation from RGList")
if(is.null(rawdata$source))
stop("Unable to read source from RGList")
rawdata<-switch(source,
agilent = rawdata<-rawdata[with(rawdata$genes,order(Row,Col)),],
genepix = rawdata<-rawdata[with(rawdata$genes,order(Block,Row,Column)),],
ae1 = rawdata<-rawdata[with(rawdata$genes,order(metaRow,metaColumn,row,column)),],
rawdata)
#if generic user has to specify feature columns in data
return(rawdata)
}
readFeatures<-function(adf,path,procADFref=NULL){
message("ArrayExpress: Reading feature metadata from ADF")
lines2skip = skipADFheader(adf,path,!is.null(procADFref))
features = try(read.table(file.path(path, adf), row.names = NULL, blank.lines.skip = TRUE, fill = TRUE, sep="\t", na.strings=c('?','NA'), skip = lines2skip, header=TRUE, quote=""))
if('Block.Column' %in% colnames(features) & 'Reporter.Name' %in% colnames(features)){
ommittedRows = which(is.na(features[,'Block.Column']) | is.na(features[,'Reporter.Name']))
if(length(ommittedRows)!=0){
message("ArrayExpress: Ommitting NA rows from ADF")
features = features[-ommittedRows,]
}
}
if(!is.null(procADFref)){
if(procADFref %in% colnames(features))
rownames(features) = features[,procADFref]
else{
repCol = getSDRFcolumn("reporter",colnames(features))
if(length(repCol) != 0)
repCol= repCol[1]
else
repCol = getSDRFcolumn("composite",colnames(features))
if(length(repCol) != 0)
repCol = repCol[1]
else
repCol = NULL
if(!is.null(repCol))
rownames(features) = features[[repCol]]
}
}
#Sort ADF features by columns Block row/Block column/Row/Column (only applicable for raw data exps, processed data is ordered by reporter/composite name)
if("Block.Row" %in% colnames(features))
features = features[with(features,order(Block.Row,Block.Column,Row,Column)),]
#Row names of featureData must match row names of the matrix / matricies in assayData
# ri1 = grep("reporter.identifier|reporter.name", colnames(adff), ignore.case=TRUE)
# ri2 = grep("reporter.identifier|reporter.name", colnames(fn), ignore.case=TRUE)
# if(all(adff2[,ri1] == fn[,ri2]))
# featureData(eset) = new("AnnotatedDataFrame",adff2)
# else stop("Do not manage to map the reporter identifier between the annotation and the data files.\n")
return(new("AnnotatedDataFrame",features))
}
## Assign experiment Data
## By Juok Cho
readExperimentData = function(idf, path){
idffile = scan(file.path(path,idf),character(),sep = "\n",encoding="UTF-8")
idf.data = list()
for(g in idffile) {
e = unlist(strsplit(g,"\t"))
key = e[1]
if(length(e)>1)
values = e[2:length(e)]
else
values = NA
idf.data[[key]] = values
}
## making key matches #
## (Person Last Name, Person First Name, Person Mid Initials), Person Email, Person Phone, Person Address, Person Affiliation,
Person_Name = c(idf.data$"Person First Name", idf.data$"Person Last Name",idf.data$"Person Mid Initials")
Personal_contact = c(idf.data$"Person Email", idf.data$"Person Phone", idf.data$"Person Address")
## making experimentData object #
SubmitterIndex = which(idf.data$"Person Roles"=="submitter")
experimentData = new("MIAME",
name = as.character(paste(idf.data$"Person Last Name"[SubmitterIndex],", ",idf.data$"Person First Name"[SubmitterIndex], sep = "")), #performer
lab = as.character(idf.data$"Person Affiliation"[SubmitterIndex]) , #Person Affiliation
contact = as.character(idf.data$"Person Email"[SubmitterIndex]), # Person Email(Person Phone, Person Address)
title = as.character(idf.data$"Investigation Title") , #description #Investigation Title
##abstract= "", #not provided in the idf.data
##url = "",
other = list(
accession = gsub(".sdrf.txt","",idf.data$"SDRF File"), #Experiment Name
identifier = gsub(".sdrf.txt","",idf.data$"SDRF File"), #Experiment Name
##Experimental Factor Type
experimentalFactor = c(idf.data$"Experimental Factor Type"),
##Experimental Design
type = c(idf.data$"Experimental Design")
#measurementType = experimentData(eset)@other$measurementType #from processed data.zip depending on user answer about QT type
)
)
#experimentData(eset) = experimentData
return(experimentData)
}
skipADFheader<-function(adf,path,proc=F){
if(!proc)
columns = list('Block Column','Block Row','Column','Row')
else
columns = list('Composite Element Name')
con = file(file.path(path, adf), "r")
on.exit(close(con))
Found = FALSE
i = 0
repeat {
i = i+1
txt <- readLines(con,n=1)
if(!length(txt))
stop("Failed to recognize ADF file format")
Found = TRUE
for(a in columns)
Found = Found && length(grep(a,txt))
Found2 = length(grep("^Reporter[[:punct:]|[:blank:]]*Name",txt,ignore.case=TRUE))
if(Found || Found2)
break
}
return(i-1)
}
getPhenoDataPerAD<-function(ad,ph,dataFiles){
phenoData = pData(ph)
arrayDataCol = getSDRFcolumn("ArrayDataFile",varLabels(ph))
arrayDesignRefCol = getSDRFcolumn("ArrayDesignREF",varLabels(ph))
if(length(arrayDataCol)==0)
stop("Cannot find 'Array.Data.File' column in SDRF. Experiment uses multiple array designs. Cannot distinguish arrays with similar array design.")
if(length(arrayDesignRefCol)==0)
stop("Cannot find 'Array.Design.REF' column in SDRF. Experiment uses multiple array designs. Cannot distinguish arrays with similar array design.")
if(length(phenoData[phenoData[arrayDesignRefCol]==ad,arrayDataCol]) == 0)
stop("Cannot find array data file names in the sdrf file. Experiment uses multiple array designs. Cannot distinguish arrays with similar array design.")
#Subselect data files for current ArrayDesign REF
selectFiles = phenoData[phenoData[arrayDesignRefCol]==ad,arrayDataCol]
if(!all(selectFiles %in% dataFiles)){
stop("Some or all data files for ",ad," array are missing.")
}
#subselect phenoData Frame for files
ph = ph[phenoData[arrayDesignRefCol]==ad]
phenoData = pData(ph)
return(list(pheno=ph,dataFiles=selectFiles))
}
getDataFormat=function(path,files){
if(length(grep(".cel",files, ignore.case = TRUE)) == length(files)){
return("affy")
}
else{
#Retrieve Column names from first data file
allcnames = scan(file.path(path,files[1]),what = "",nlines = 200, sep = "\t",quiet=TRUE)
allcnamesL = try(tolower(gsub("^\\s","",allcnames)),silent=TRUE)
if(inherits(allcnamesL, 'try-error')){
allcnames = scan(file.path(path,files[1]),what = "",nlines = 200, sep = "\t",quiet=TRUE,encoding="latin1")
allcnamesL = try(tolower(gsub("^\\s","",allcnames)))
if(inherits(allcnamesL, 'try-error')){
allcnamesL = allcnames
}
}
#Find source of data
for(source in names(headers)){
allthere<-tolower(headers[[source]]) %in% allcnamesL
if(all(allthere))
return(source)
}
}
#Unable to detect source
allcnames = scan(file.path(path,files[1]),what = "",nlines = 1, sep = "\n",quiet=TRUE)
return("unknown")
#stop("Unable to recognize data file format. First line:\n",allcnames)
}
getDataColsForAE1 = function(path,files){
url2 = "http://sourceforge.net/p/tab2mage/code/HEAD/tree/trunk/Tab2MAGE/lib/ArrayExpress/Datafile/QT_list.txt?format=raw"
qt = try(read.table(url2, sep = "\t", quote = "",
check.names = FALSE, fill = TRUE,
comment.char = "#",
stringsAsFactors = FALSE,
encoding = "UTF-8")) ##read the QT file from the web
if(inherits(qt, "try-error"))
qt = try(read.table(
file.path(system.file("doc", package = "ArrayExpress"),"QT_list.txt"),
sep = "\t", quote = "",
check.names = FALSE, fill = TRUE,
comment.char = "#",
stringsAsFactors = FALSE,
encoding = "UTF-8")) ##read the QT file from the package
scanners = grep(">>>",qt[,1],value = TRUE) ## list all the scanner names
sl = grep(">>>",qt[,1]) ## list all the line numbers wherea scanner type starts
scanners = gsub(">","",scanners)
## Parsing the first line of the expression file
allcnames = scan(file.path(path,files[1]),what = "",nlines = 1, sep = "\t",quiet=TRUE)
## Looking for the right column to use
scanname = allcnames[grep(":",allcnames)]
if(length(grep("Database|Reporter",scanname)) != 0)
scanname = scanname[-grep("Database|Reporter",scanname)]
##Feature is a problem because of Feature Extraction
feature = grep("^Feature^",scanname)
fe = grep("Feature Extraction",scanname)
if(length(feature) != 0)
scanname = scanname[-feature[!feature %in% fe]]
##Ready to read data
if(length(scanname) == 0)
stop(sprintf("No scanner name is given. It is not possible to handle such a case. Try to set the argument 'dataCols' by choosing among the following columns names: \n") ,
sprintf("\"%s\" \n",allcnames))
##Image Analysis Program
software = unique(sapply(seq_len(length(scanname)), function(i) strsplit(scanname,":")[[i]][1]))
st = NULL
for(x in software){
if(length(grep(x, scanners)) != 0){
st = x
break
}
}
#if(length(grep(st, scanners)) == 0)
if(is.null(st))
stop(sprintf("Scanner name is, ",software,". This scanner type is not valid. \nTry to set the argument 'dataCols' by choosing among the following columns names: \n", st),sprintf("\"%s\" \n",scanname))
if(length(st) != 1)
stop(sprintf("%s scanner names are given ( ",length(st)), sprintf("\"%s\" ",st), sprintf("). It is not possible to handle such a case. Try to set the argument 'dataCols' by choosing among the following columns names: \n") ,sprintf("\"%s\" \n",scanname))
if(length(grep(st, scanners)) > 1)
stop(sprintf("Scanner name can be '%s'. \nTry to set the argument 'dataCols' by choosing among the following columns names: \n", scanners[grep(st, scanners)]),sprintf("\"%s\" \n",scanname))
gs = qt[((sl[grep(st,scanners)]+1):(sl[grep(st,scanners)+1]-1)),] ## extract the QTs of the specific scanner type
foreground = gs[(gs[,4] == "MeasuredSignal" & (is.na(gs[,5]) | gs[,5] == 0)),c(1,7)] ## the colnames to use in the read.column
background = gs[(gs[,4] == "MeasuredSignal" & (gs[,5] == 1)),c(1,7)] ## the colnames to use in the read.column
foreground[,1] = paste(st,":",foreground[,1],sep = "")
colnamesf = foreground[which(foreground[,1] %in% allcnames),]
df = dim(colnamesf)
if(dim(background)[1] != 0){
background[,1] = paste(st,":",background[,1],sep = "")
colnamesb = background[which(background[,1] %in% allcnames),]
db = dim(colnamesb)
}else
db = 0
if(length(files) != 1){
if(!all(sapply(2:length(files), function(i) readLines(file.path(path,files[1]),1) == readLines(file.path(path,files[i]),1))))
warning(sprintf("The files do not all have the same headings whereas the array design is the same. It may cause the object not being created."))
}
#Two channel data
if(df[1] == 2){
rawcol = if(db[1] == 2)
list(R = colnamesf[colnamesf[,2] == "Cy5",1],
G = colnamesf[colnamesf[,2] == "Cy3",1],
Rb = colnamesb[colnamesb[,2] == "Cy5",1],
Gb = colnamesb[colnamesb[,2] == "Cy3",1])
else
list(R = colnamesf[colnamesf[,2] == "Cy5",1],
G = colnamesf[colnamesf[,2] == "Cy3",1])
if(length(rawcol) == 0 || (0 %in% sapply(seq_len(length(rawcol)), function(i) length(rawcol[[i]]))))
stop(sprintf("The known column names for this scanner are not in the heading of the files.\nTry to set the argument 'rawcol' by choosing among the following columns names: \n"),
sprintf("\"%s\" \n",scanname))
}
## one channel data
if(df[1] == 1){
rawcol = if(db != 0)
list(G = colnamesf[,1],
Gb = colnamesb[,1])
else
list(G = colnamesf[,1])
}
if(df[1] == 0)
stop(sprintf("None of the columns names of the expression files is matching a valid known quantitation type.\nTry to set the argument 'rawcol' by choosing among the following columns names: \n"), sprintf("\"%s\" \n",scanname))
if(df[1] > 2)
stop(sprintf("There are too many columns that could be read in the files.\n Try to set the argument 'rawcol' by choosing among the following columns names: \n"),sprintf("\"%s\" \n",scanname))
return(rawcol)
}
## assign phenoData to Nchannelset
preparePhenoDataFor2channel = function(ph,files){
#if(length(unique(tolower(ph[[labelCol]])))==2){
arrayFilesNum = length(unique(ph[[arrayDataCol]]))
si = pData(ph)[1:(arrayFilesNum*2),]
lab = split(si,si[,"Label"])
if(nrow(lab[[1]]) != nrow(lab[[2]])){
stop("Number of CY3/CY5 is not equal")
}
#Reorder rows in each group (Cy3,Cy5) to the same order
lab[[1]] = lab[[1]][order(lab[[1]][,arrayDataCol]),]
lab[[2]] = lab[[2]][order(lab[[2]][,arrayDataCol]),]
same = which(lapply(1:ncol(lab[[1]]), function(i) all(lab[[1]][i] == lab[[2]][i])) == TRUE)
all = lab[[1]][same]
gspe = lab[[1]][-same]
colnames(gspe) = paste(colnames(gspe),names(lab)[1],sep = ".")
rspe = lab[[2]][-same]
colnames(rspe) = paste(colnames(rspe),names(lab)[2],sep = ".")
metaData = data.frame(labelDescription = c(rep("_ALL_",ncol(all)),rep("G",ncol(gspe)),rep("R",ncol(rspe))))
ph = new("AnnotatedDataFrame", data = cbind(all,gspe,rspe), varMetadata = metaData)
arrayDataCol = getSDRFcolumn("ArrayDataFile",varLabels(ph))
rownames(pData(ph)) = gsub(".[a-z][a-z][a-z]$","",ph[[arrayDataCol]],ignore.case=T)
#}
return(ph)
}
getSDRFcolumn = function(col,headers){
pattern<-switch(col,
ArrayDataFile = "^Array[[:punct:]|[:blank:]]*Data[[:punct:]|[:blank:]]*File",
ArrayDesignREF = "^Array[[:punct:]|[:blank:]]*Design[[:punct:]|[:blank:]]*REF",
ArrayDataMatrixFile = "^Array[[:punct:]|[:blank:]]*Data[[:punct:]|[:blank:]]*Matrix[[:punct:]|[:blank:]]*File",
label = "^Label$",
factorValues = "^Factor[[:punct:]|[:blank:]]*Value",
DerivedArrayMatrix = "^Derived[[:punct:]|[:blank:]]*Array[[:punct:]|[:blank:]]*Data[[:punct:]|[:blank:]]*Matrix[[:punct:]|[:blank:]]*File",
DerivedArrayFile = "^Derived[[:punct:]|[:blank:]]*Array[[:punct:]|[:blank:]]*Data[[:punct:]|[:blank:]]*File",
reporter = "^Reporter[[:punct:]|[:blank:]]*[Name | Identifier]",
composite = "^Composite[[:punct:]|[:blank:]]*Element[[:punct:]|[:blank:]]*[Name | Identifier]")
colIndex = grep(pattern,headers,ignore.case = TRUE)
return(colIndex)
}
## remove all downloaded files
cleanupAE = function(mageFiles){
path = mageFiles$path
try(file.remove(file.path(path, mageFiles$rawFiles)))
try(file.remove(file.path(path, mageFiles$processedFiles)))
try(file.remove(file.path(path, mageFiles$sdrf)))
try(file.remove(file.path(path, mageFiles$idf)))
try(file.remove(file.path(path, mageFiles$adf)))
try(file.remove(file.path(path, mageFiles$rawArchive)))
try(file.remove(file.path(path, mageFiles$processedArchive)))
}
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Defines functions cleanupAE getSDRFcolumn preparePhenoDataFor2channel getDataColsForAE1 getDataFormat getPhenoDataPerAD skipADFheader readExperimentData readFeatures readAEdata readPhenoData isOneChannel
# TODO: Add comment
#
# Author: iemam
###############################################################################
headers<-list(
ae1=c("metaColumn","metaRow","row","column"),
genepix=c("Block","Column","Row","X","Y"),
arrayvision=c("Primary","Secondary"),
agilent=c("Row","Col","PositionX","PositionY"),
scanalyze=c("GRID","COL","ROW","LEFT","TOP","RIGHT","BOT"),
scanarray=c('Array Column','Array Row','Spot Column','Spot Row','X','Y'),
quantarray=c('Array Column', 'Array Row', 'Column', 'Row'),
spotfinder=c("MC","MR","SC","SR","C","R"),
mev=c("MC","MR","C","R","UID"),
codelink=c("Logical_row","Logical_col","Center_X","Center_Y"),
bluefuse=c("COL","ROW","SUBGRIDCOL","SUBGRIDROW"),
UCSFSpot=c("Arr-colx","Arr-rowy","Spot-colx","Spot-rowy"),
NimbleScanFeature=c("X","Y","PROBE_ID","X_PIXEL","Y_PIXEL"),
NimblegenNASA=c("X_BC","Y_BC","Feature_ID","ProbID_BC"),
imagene=c('Meta Column', 'Meta Row', 'Column', 'Row', 'Field', 'Gene ID'),
ImaGene3=c("Meta_col","Meta_row","Sub_col","Sub_row","Name","Selected"),
ImaGene7=c("Block","Column","Row","Ch1 XCoord","Ch1 YCoord", "Ch2 XCoord", "Ch2 YCoord"),
ImaGeneFields=c("Field","Column","Row","XCoord","YCoord"),
CSIRO_Spot=c("grid_c","grid_r","spot_c","spot_r","indexs")
#add illumina
)
isOneChannel = function(sdrf,path){
ph = try(read.AnnotatedDataFrame(sdrf, path = path, row.names = NULL, blank.lines.skip = TRUE, fill = TRUE, varMetadata.char = "$", quote="\""))
labelCol = getSDRFcolumn("label",varLabels(ph))
if(length(labelCol)==0)
return(TRUE) # assume 1-color if no label reported - we warn the user in readPhenoData
else
return(length(unique(tolower(ph[[labelCol]])))==1)
}
readPhenoData = function(sdrf,path){
message("ArrayExpress: Reading pheno data from SDRF")
ph = try(read.AnnotatedDataFrame(sdrf, path = path, row.names = NULL, blank.lines.skip = TRUE, fill = TRUE, varMetadata.char = "$", quote="\""))
arrayDataCol = getSDRFcolumn("ArrayDataFile",varLabels(ph))
labelCol = getSDRFcolumn("label",varLabels(ph))
if(length(arrayDataCol)==0)
warning("ArrayExpress: Cannot find 'Array Data File' column in SDRF. Object might not be created correctly.")
if(length(labelCol)==0)
warning("ArrayExpress: Cannot find 'Label' column in SDRF. Object might not be created correctly.")
ph = ph[gsub(" ", "", ph$Array.Data.File) != ""]
sampleNames(ph) = ph$Array.Data.File
ph@varMetadata['Array.Data.File','labelDescription'] = "Index"
ph@varMetadata['Array.Data.File','channel'] = as.factor("_ALL_")
#Remove empty rows from pheno data
emptylines = which(sapply(seq_len(nrow(pData(ph))), function(i) all(pData(ph)[i,] == "",na.rm = TRUE)))
if(length(emptylines) != 0)
pData(ph) = pData(ph)[-emptylines,]
phenoData = pData(ph)
if(length(arrayDataCol)!=0 && length(labelCol)!=0){
#filter out duplicated rows where multiple derived data files are available per one array data file
ph=ph[!duplicated(phenoData[,c(arrayDataCol,labelCol)])]
}
#treat SDRF for two channel experiments
if(length(labelCol)==1 && length(unique(tolower(ph[[labelCol]])))==2){
arrayFilesNum = length(unique(ph[[arrayDataCol]]))
si = pData(ph)[1:(arrayFilesNum*2),]
lab = split(si,si[,"Label"])
if(nrow(lab[[1]]) != nrow(lab[[2]])){
stop("Number of CY3/CY5 is not equal")
}
#Reorder rows in each group (Cy3,Cy5) to the same order
lab[[1]] = lab[[1]][order(lab[[1]][,arrayDataCol]),]
lab[[2]] = lab[[2]][order(lab[[2]][,arrayDataCol]),]
same = which(lapply(1:ncol(lab[[1]]), function(i) all(lab[[1]][i] == lab[[2]][i])) == TRUE)
all = lab[[1]][same]
gspe = lab[[1]][-same]
colnames(gspe) = paste(colnames(gspe),names(lab)[1],sep = ".")
rspe = lab[[2]][-same]
colnames(rspe) = paste(colnames(rspe),names(lab)[2],sep = ".")
metaData = data.frame(labelDescription = c(rep("_ALL_",ncol(all)),rep("G",ncol(gspe)),rep("R",ncol(rspe))))
ph = new("AnnotatedDataFrame", data = cbind(all,gspe,rspe), varMetadata = metaData)
arrayDataCol = getSDRFcolumn("ArrayDataFile",varLabels(ph))
rownames(pData(ph)) = gsub(".[a-z][a-z][a-z]$","",ph[[arrayDataCol]],ignore.case=T)
}
# if(!all(basename(files) %in% pData(ph)[,getSDRFcolumn("ArrayDataFile",varLabels(ph))]))
# warning("Some data files in the zip archive are missing from the SDRF. The object may not be built.")
return(ph)
}
readAEdata = function(path,files,dataCols,green.only){
message("ArrayExpress: Reading data files")
source = getDataFormat(path,files)
#process extra arguments passed to read.maimages
# if (!is.null(dataCols)) {
# if (length(rawcol) > 1 && !is(rawcol, "list"))
# stop("The argument 'rawcol' must be a list if multiple column name are given.")
# if (length(rawcol) == 1 && !is(rawcol, "character"))
# stop("The argument 'rawcol' must be a character if one column name is given.")
# if (is(rawcol, "list") && !("R" %in% names(rawcol) && "G" %in% names(rawcol)))
# stop("The names of the columns must contain R and G.")
# }
if(source == "affy"){
rawdata = try(oligo::read.celfiles(filenames = file.path(path,unique(files))))
if(inherits(rawdata, 'try-error')){
stop("Unable to read cel files in",path)
}
return(rawdata)
}else if(source=="ae1"){
#Old AE1 formatted data files
if (is.null(dataCols)){
dataCols= try(getDataColsForAE1(path,files))
if(inherits(dataCols,'try-error')) return()
}
rawdata = try(read.maimages(files=files,path=path,source="generic",columns=dataCols,annotation=headers$ae1))
if(!inherits(rawdata, 'try-error')) rawdata$source="ae1"
}else if(source %in% c("agilent","arrayvision","bluefuse","genepix","bluefuse","imagene","quantarray")){
#data format can be directly read by limma
rawdata = try(read.maimages(files=files,path=path,source=source,columns=dataCols,green.only=green.only))
}else if(!is.null(dataCols) && source=="unknown"){
#read generic source given columns specified by user
rawdata = try(read.maimages(files=files,path=path,source="generic",columns=dataCols,green.only=green.only))
}else
# TODO: add more formats (illumina)
stop("Unable to recognize data file format")
if(inherits(rawdata, 'try-error')){
stop("Unable to read data files in",path)
}
#reorder rows of RGList to reflect the same order in ADF as Block Row/Block Column/Row/Column
if(is.null(rawdata$genes))
stop("Unable to read probe annotation from RGList")
if(is.null(rawdata$source))
stop("Unable to read source from RGList")
rawdata<-switch(source,
agilent = rawdata<-rawdata[with(rawdata$genes,order(Row,Col)),],
genepix = rawdata<-rawdata[with(rawdata$genes,order(Block,Row,Column)),],
ae1 = rawdata<-rawdata[with(rawdata$genes,order(metaRow,metaColumn,row,column)),],
rawdata)
#if generic user has to specify feature columns in data
return(rawdata)
}
readFeatures<-function(adf,path,procADFref=NULL){
message("ArrayExpress: Reading feature metadata from ADF")
lines2skip = skipADFheader(adf,path,!is.null(procADFref))
features = try(read.table(file.path(path, adf), row.names = NULL, blank.lines.skip = TRUE, fill = TRUE, sep="\t", na.strings=c('?','NA'), skip = lines2skip, header=TRUE, quote=""))
if('Block.Column' %in% colnames(features) & 'Reporter.Name' %in% colnames(features)){
ommittedRows = which(is.na(features[,'Block.Column']) | is.na(features[,'Reporter.Name']))
if(length(ommittedRows)!=0){
message("ArrayExpress: Ommitting NA rows from ADF")
features = features[-ommittedRows,]
}
}
if(!is.null(procADFref)){
if(procADFref %in% colnames(features))
rownames(features) = features[,procADFref]
else{
repCol = getSDRFcolumn("reporter",colnames(features))
if(length(repCol) != 0)
repCol= repCol[1]
else
repCol = getSDRFcolumn("composite",colnames(features))
if(length(repCol) != 0)
repCol = repCol[1]
else
repCol = NULL
if(!is.null(repCol))
rownames(features) = features[[repCol]]
}
}
#Sort ADF features by columns Block row/Block column/Row/Column (only applicable for raw data exps, processed data is ordered by reporter/composite name)
if("Block.Row" %in% colnames(features))
features = features[with(features,order(Block.Row,Block.Column,Row,Column)),]
#Row names of featureData must match row names of the matrix / matricies in assayData
# ri1 = grep("reporter.identifier|reporter.name", colnames(adff), ignore.case=TRUE)
# ri2 = grep("reporter.identifier|reporter.name", colnames(fn), ignore.case=TRUE)
# if(all(adff2[,ri1] == fn[,ri2]))
# featureData(eset) = new("AnnotatedDataFrame",adff2)
# else stop("Do not manage to map the reporter identifier between the annotation and the data files.\n")
return(new("AnnotatedDataFrame",features))
}
## Assign experiment Data
## By Juok Cho
readExperimentData = function(idf, path){
idffile = scan(file.path(path,idf),character(),sep = "\n",encoding="UTF-8")
idf.data = list()
for(g in idffile) {
e = unlist(strsplit(g,"\t"))
key = e[1]
if(length(e)>1)
values = e[2:length(e)]
else
values = NA
idf.data[[key]] = values
}
## making key matches #
## (Person Last Name, Person First Name, Person Mid Initials), Person Email, Person Phone, Person Address, Person Affiliation,
Person_Name = c(idf.data$"Person First Name", idf.data$"Person Last Name",idf.data$"Person Mid Initials")
Personal_contact = c(idf.data$"Person Email", idf.data$"Person Phone", idf.data$"Person Address")
## making experimentData object #
SubmitterIndex = which(idf.data$"Person Roles"=="submitter")
experimentData = new("MIAME",
name = as.character(paste(idf.data$"Person Last Name"[SubmitterIndex],", ",idf.data$"Person First Name"[SubmitterIndex], sep = "")), #performer
lab = as.character(idf.data$"Person Affiliation"[SubmitterIndex]) , #Person Affiliation
contact = as.character(idf.data$"Person Email"[SubmitterIndex]), # Person Email(Person Phone, Person Address)
title = as.character(idf.data$"Investigation Title") , #description #Investigation Title
##abstract= "", #not provided in the idf.data
##url = "",
other = list(
accession = gsub(".sdrf.txt","",idf.data$"SDRF File"), #Experiment Name
identifier = gsub(".sdrf.txt","",idf.data$"SDRF File"), #Experiment Name
##Experimental Factor Type
experimentalFactor = c(idf.data$"Experimental Factor Type"),
##Experimental Design
type = c(idf.data$"Experimental Design")
#measurementType = experimentData(eset)@other$measurementType #from processed data.zip depending on user answer about QT type
)
)
#experimentData(eset) = experimentData
return(experimentData)
}
skipADFheader<-function(adf,path,proc=F){
if(!proc)
columns = list('Block Column','Block Row','Column','Row')
else
columns = list('Composite Element Name')
con = file(file.path(path, adf), "r")
on.exit(close(con))
Found = FALSE
i = 0
repeat {
i = i+1
txt <- readLines(con,n=1)
if(!length(txt))
stop("Failed to recognize ADF file format")
Found = TRUE
for(a in columns)
Found = Found && length(grep(a,txt))
Found2 = length(grep("^Reporter[[:punct:]|[:blank:]]*Name",txt,ignore.case=TRUE))
if(Found || Found2)
break
}
return(i-1)
}
getPhenoDataPerAD<-function(ad,ph,dataFiles){
phenoData = pData(ph)
arrayDataCol = getSDRFcolumn("ArrayDataFile",varLabels(ph))
arrayDesignRefCol = getSDRFcolumn("ArrayDesignREF",varLabels(ph))
if(length(arrayDataCol)==0)
stop("Cannot find 'Array.Data.File' column in SDRF. Experiment uses multiple array designs. Cannot distinguish arrays with similar array design.")
if(length(arrayDesignRefCol)==0)
stop("Cannot find 'Array.Design.REF' column in SDRF. Experiment uses multiple array designs. Cannot distinguish arrays with similar array design.")
if(length(phenoData[phenoData[arrayDesignRefCol]==ad,arrayDataCol]) == 0)
stop("Cannot find array data file names in the sdrf file. Experiment uses multiple array designs. Cannot distinguish arrays with similar array design.")
#Subselect data files for current ArrayDesign REF
selectFiles = phenoData[phenoData[arrayDesignRefCol]==ad,arrayDataCol]
if(!all(selectFiles %in% dataFiles)){
stop("Some or all data files for ",ad," array are missing.")
}
#subselect phenoData Frame for files
ph = ph[phenoData[arrayDesignRefCol]==ad]
phenoData = pData(ph)
return(list(pheno=ph,dataFiles=selectFiles))
}
getDataFormat=function(path,files){
if(length(grep(".cel",files, ignore.case = TRUE)) == length(files)){
return("affy")
}
else{
#Retrieve Column names from first data file
allcnames = scan(file.path(path,files[1]),what = "",nlines = 200, sep = "\t",quiet=TRUE)
allcnamesL = try(tolower(gsub("^\\s","",allcnames)),silent=TRUE)
if(inherits(allcnamesL, 'try-error')){
allcnames = scan(file.path(path,files[1]),what = "",nlines = 200, sep = "\t",quiet=TRUE,encoding="latin1")
allcnamesL = try(tolower(gsub("^\\s","",allcnames)))
if(inherits(allcnamesL, 'try-error')){
allcnamesL = allcnames
}
}
#Find source of data
for(source in names(headers)){
allthere<-tolower(headers[[source]]) %in% allcnamesL
if(all(allthere))
return(source)
}
}
#Unable to detect source
allcnames = scan(file.path(path,files[1]),what = "",nlines = 1, sep = "\n",quiet=TRUE)
return("unknown")
#stop("Unable to recognize data file format. First line:\n",allcnames)
}
getDataColsForAE1 = function(path,files){
url2 = "http://sourceforge.net/p/tab2mage/code/HEAD/tree/trunk/Tab2MAGE/lib/ArrayExpress/Datafile/QT_list.txt?format=raw"
qt = try(read.table(url2, sep = "\t", quote = "",
check.names = FALSE, fill = TRUE,
comment.char = "#",
stringsAsFactors = FALSE,
encoding = "UTF-8")) ##read the QT file from the web
if(inherits(qt, "try-error"))
qt = try(read.table(
file.path(system.file("doc", package = "ArrayExpress"),"QT_list.txt"),
sep = "\t", quote = "",
check.names = FALSE, fill = TRUE,
comment.char = "#",
stringsAsFactors = FALSE,
encoding = "UTF-8")) ##read the QT file from the package
scanners = grep(">>>",qt[,1],value = TRUE) ## list all the scanner names
sl = grep(">>>",qt[,1]) ## list all the line numbers wherea scanner type starts
scanners = gsub(">","",scanners)
## Parsing the first line of the expression file
allcnames = scan(file.path(path,files[1]),what = "",nlines = 1, sep = "\t",quiet=TRUE)
## Looking for the right column to use
scanname = allcnames[grep(":",allcnames)]
if(length(grep("Database|Reporter",scanname)) != 0)
scanname = scanname[-grep("Database|Reporter",scanname)]
##Feature is a problem because of Feature Extraction
feature = grep("^Feature^",scanname)
fe = grep("Feature Extraction",scanname)
if(length(feature) != 0)
scanname = scanname[-feature[!feature %in% fe]]
##Ready to read data
if(length(scanname) == 0)
stop(sprintf("No scanner name is given. It is not possible to handle such a case. Try to set the argument 'dataCols' by choosing among the following columns names: \n") ,
sprintf("\"%s\" \n",allcnames))
##Image Analysis Program
software = unique(sapply(seq_len(length(scanname)), function(i) strsplit(scanname,":")[[i]][1]))
st = NULL
for(x in software){
if(length(grep(x, scanners)) != 0){
st = x
break
}
}
#if(length(grep(st, scanners)) == 0)
if(is.null(st))
stop(sprintf("Scanner name is, ",software,". This scanner type is not valid. \nTry to set the argument 'dataCols' by choosing among the following columns names: \n", st),sprintf("\"%s\" \n",scanname))
if(length(st) != 1)
stop(sprintf("%s scanner names are given ( ",length(st)), sprintf("\"%s\" ",st), sprintf("). It is not possible to handle such a case. Try to set the argument 'dataCols' by choosing among the following columns names: \n") ,sprintf("\"%s\" \n",scanname))
if(length(grep(st, scanners)) > 1)
stop(sprintf("Scanner name can be '%s'. \nTry to set the argument 'dataCols' by choosing among the following columns names: \n", scanners[grep(st, scanners)]),sprintf("\"%s\" \n",scanname))
gs = qt[((sl[grep(st,scanners)]+1):(sl[grep(st,scanners)+1]-1)),] ## extract the QTs of the specific scanner type
foreground = gs[(gs[,4] == "MeasuredSignal" & (is.na(gs[,5]) | gs[,5] == 0)),c(1,7)] ## the colnames to use in the read.column
background = gs[(gs[,4] == "MeasuredSignal" & (gs[,5] == 1)),c(1,7)] ## the colnames to use in the read.column
foreground[,1] = paste(st,":",foreground[,1],sep = "")
colnamesf = foreground[which(foreground[,1] %in% allcnames),]
df = dim(colnamesf)
if(dim(background)[1] != 0){
background[,1] = paste(st,":",background[,1],sep = "")
colnamesb = background[which(background[,1] %in% allcnames),]
db = dim(colnamesb)
}else
db = 0
if(length(files) != 1){
if(!all(sapply(2:length(files), function(i) readLines(file.path(path,files[1]),1) == readLines(file.path(path,files[i]),1))))
warning(sprintf("The files do not all have the same headings whereas the array design is the same. It may cause the object not being created."))
}
#Two channel data
if(df[1] == 2){
rawcol = if(db[1] == 2)
list(R = colnamesf[colnamesf[,2] == "Cy5",1],
G = colnamesf[colnamesf[,2] == "Cy3",1],
Rb = colnamesb[colnamesb[,2] == "Cy5",1],
Gb = colnamesb[colnamesb[,2] == "Cy3",1])
else
list(R = colnamesf[colnamesf[,2] == "Cy5",1],
G = colnamesf[colnamesf[,2] == "Cy3",1])
if(length(rawcol) == 0 || (0 %in% sapply(seq_len(length(rawcol)), function(i) length(rawcol[[i]]))))
stop(sprintf("The known column names for this scanner are not in the heading of the files.\nTry to set the argument 'rawcol' by choosing among the following columns names: \n"),
sprintf("\"%s\" \n",scanname))
}
## one channel data
if(df[1] == 1){
rawcol = if(db != 0)
list(G = colnamesf[,1],
Gb = colnamesb[,1])
else
list(G = colnamesf[,1])
}
if(df[1] == 0)
stop(sprintf("None of the columns names of the expression files is matching a valid known quantitation type.\nTry to set the argument 'rawcol' by choosing among the following columns names: \n"), sprintf("\"%s\" \n",scanname))
if(df[1] > 2)
stop(sprintf("There are too many columns that could be read in the files.\n Try to set the argument 'rawcol' by choosing among the following columns names: \n"),sprintf("\"%s\" \n",scanname))
return(rawcol)
}
## assign phenoData to Nchannelset
preparePhenoDataFor2channel = function(ph,files){
#if(length(unique(tolower(ph[[labelCol]])))==2){
arrayFilesNum = length(unique(ph[[arrayDataCol]]))
si = pData(ph)[1:(arrayFilesNum*2),]
lab = split(si,si[,"Label"])
if(nrow(lab[[1]]) != nrow(lab[[2]])){
stop("Number of CY3/CY5 is not equal")
}
#Reorder rows in each group (Cy3,Cy5) to the same order
lab[[1]] = lab[[1]][order(lab[[1]][,arrayDataCol]),]
lab[[2]] = lab[[2]][order(lab[[2]][,arrayDataCol]),]
same = which(lapply(1:ncol(lab[[1]]), function(i) all(lab[[1]][i] == lab[[2]][i])) == TRUE)
all = lab[[1]][same]
gspe = lab[[1]][-same]
colnames(gspe) = paste(colnames(gspe),names(lab)[1],sep = ".")
rspe = lab[[2]][-same]
colnames(rspe) = paste(colnames(rspe),names(lab)[2],sep = ".")
metaData = data.frame(labelDescription = c(rep("_ALL_",ncol(all)),rep("G",ncol(gspe)),rep("R",ncol(rspe))))
ph = new("AnnotatedDataFrame", data = cbind(all,gspe,rspe), varMetadata = metaData)
arrayDataCol = getSDRFcolumn("ArrayDataFile",varLabels(ph))
rownames(pData(ph)) = gsub(".[a-z][a-z][a-z]$","",ph[[arrayDataCol]],ignore.case=T)
#}
return(ph)
}
getSDRFcolumn = function(col,headers){
pattern<-switch(col,
ArrayDataFile = "^Array[[:punct:]|[:blank:]]*Data[[:punct:]|[:blank:]]*File",
ArrayDesignREF = "^Array[[:punct:]|[:blank:]]*Design[[:punct:]|[:blank:]]*REF",
ArrayDataMatrixFile = "^Array[[:punct:]|[:blank:]]*Data[[:punct:]|[:blank:]]*Matrix[[:punct:]|[:blank:]]*File",
label = "^Label$",
factorValues = "^Factor[[:punct:]|[:blank:]]*Value",
DerivedArrayMatrix = "^Derived[[:punct:]|[:blank:]]*Array[[:punct:]|[:blank:]]*Data[[:punct:]|[:blank:]]*Matrix[[:punct:]|[:blank:]]*File",
DerivedArrayFile = "^Derived[[:punct:]|[:blank:]]*Array[[:punct:]|[:blank:]]*Data[[:punct:]|[:blank:]]*File",
reporter = "^Reporter[[:punct:]|[:blank:]]*[Name | Identifier]",
composite = "^Composite[[:punct:]|[:blank:]]*Element[[:punct:]|[:blank:]]*[Name | Identifier]")
colIndex = grep(pattern,headers,ignore.case = TRUE)
return(colIndex)
}
## remove all downloaded files
cleanupAE = function(mageFiles){
path = mageFiles$path
try(file.remove(file.path(path, mageFiles$rawFiles)))
try(file.remove(file.path(path, mageFiles$processedFiles)))
try(file.remove(file.path(path, mageFiles$sdrf)))
try(file.remove(file.path(path, mageFiles$idf)))
try(file.remove(file.path(path, mageFiles$adf)))
try(file.remove(file.path(path, mageFiles$rawArchive)))
try(file.remove(file.path(path, mageFiles$processedArchive)))
}
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