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Load FANTOM5 data using getCTSS().
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Also rename function parameter, because "source" is already a function name.

See also #78
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@charles-plessy
charles-plessy committed Jun 27, 2023
1 parent 2afbddc commit 8dcec18
Showing 1 changed file with 38 additions and 57 deletions.
95 changes: 38 additions & 57 deletions R/ImportMethods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -657,19 +657,16 @@ setMethod( "getCTSS", "CAGEexp"
#' @export

setGeneric("importPublicData",
function(source = c("FANTOM5", "FANTOM3and4", "ENCODE", "ZebrafishDevelopment"),
function(origin = c("FANTOM5", "FANTOM3and4", "ENCODE", "ZebrafishDevelopment"),
dataset,
group,
sample)
standardGeneric("importPublicData"))

setMethod("importPublicData", signature(source = "character", dataset = "character", sample = "character"),
.importPublicData(source, dataset, group, sample))
.importPublicData <- function(origin = c("FANTOM5", "FANTOM3and4", "ENCODE", "ZebrafishDevelopment"), dataset, group, sample) {
# origin <- match.arg(origin)

.importPublicData <- function(source = c("FANTOM5", "FANTOM3and4", "ENCODE", "ZebrafishDevelopment"), dataset, group, sample) {
source <- match.arg(source)

if(source == "ENCODE"){
if(origin == "ENCODE"){

if("ENCODEprojectCAGE" %in% rownames(installed.packages()) == FALSE){
stop("Requested CAGE data package is not installed! Please install and load the ENCODEprojectCAGE package, which is available for download from http://promshift.genereg.net/CAGEr/PackageSource/.")
Expand Down Expand Up @@ -787,7 +784,7 @@ setMethod("importPublicData", signature(source = "character", dataset = "charact
}


}else if(source == "FANTOM3and4"){
}else if(origin == "FANTOM3and4"){

if("FANTOM3and4CAGE" %in% rownames(installed.packages()) == FALSE){
stop("Requested CAGE data package is not installed! Please install and load the FANTOM3and4CAGE package available from Bioconductor.")
Expand Down Expand Up @@ -900,60 +897,15 @@ setMethod("importPublicData", signature(source = "character", dataset = "charact



}else if (source == "FANTOM5"){

if(length(dataset) != 1){
stop("For FANTOM5 only one dataset can be specified and it can be either 'human' or 'mouse'!")
}else if(!(dataset %in% c("human", "mouse"))){
stop("For FANTOM5, dataset can be either 'human' or 'mouse'!")
}
if(dataset == "human"){
FANTOM5humanSamples <- NULL
data("FANTOM5humanSamples", envir = environment())
samples.info <- FANTOM5humanSamples
genome.name <- "BSgenome.Hsapiens.UCSC.hg19"
}else if(dataset == "mouse"){
FANTOM5mouseSamples <- NULL
data("FANTOM5mouseSamples", envir = environment())
samples.info <- FANTOM5mouseSamples
genome.name <- "BSgenome.Mmusculus.UCSC.mm9"
}

if(!(all(sample %in% samples.info$sample))){
stop(paste("Some sample names cannot be found for the specified dataset! Call data(FANTOM5", dataset, "Samples) and check the 'sample' column for valid sample names!", sep = ""))
}



for(i in c(1:length(sample))){

message("Fetching sample: ", sample[i], "...")
sample.url <- samples.info[samples.info$sample == sample[i], "data_url"]
con <- gzcon(url(paste(sample.url)))
ctss <- scan(con, what = list(character(), NULL, integer(), NULL, integer(), character()))
ctss.df <- data.table(chr = ctss[[1]], pos = ctss[[3]], strand = ctss[[6]], tagCount = ctss[[5]])
setnames(ctss.df, c("chr", "pos", "strand", sample[i]))
setkeyv(ctss.df, cols = c("chr", "pos", "strand"))
if(i == 1){
ctss.table <- ctss.df
}else{
message("Adding sample to CTSS table...\n")
ctss.table <- merge(ctss.table, ctss.df, all.x = T, all.y = T)
ctss.table[is.na(ctss.table)] <- 0
}

}

ctssTable <- data.frame(ctss.table, stringsAsFactors = F, check.names = F)


} else if (source == "ZebrafishDevelopment") .importPublicData_ZF (group = group, sample = sample)
}else if (origin == "FANTOM5") {
.importPublicData_F5 (dataset = dataset, group = group, sample = sample)
}else if (origin == "ZebrafishDevelopment") .importPublicData_ZF (group = group, sample = sample)

rownames(ctssTable) <- c(1:nrow(ctssTable))

sample.labels <- colnames(ctssTable)[4:ncol(ctssTable)]
names(sample.labels) <- rainbow(n = length(sample.labels))
myCAGEset <- new("CAGEset", genomeName = genome.name, inputFiles = paste(source, sample.labels, sep = "__"), inputFilesType = source, sampleLabels = sample.labels)
myCAGEset <- new("CAGEset", genomeName = genome.name, inputFiles = paste(origin, sample.labels, sep = "__"), inputFilesType = origin, sampleLabels = sample.labels)
myCAGEset@librarySizes <- as.integer(colSums(ctssTable[,4:ncol(ctssTable),drop=FALSE]))
myCAGEset@CTSScoordinates <- ctssTable[, c("chr", "pos", "strand")]
myCAGEset@tagCountMatrix <- ctssTable[,4:ncol(ctssTable),drop=FALSE]
Expand All @@ -962,6 +914,32 @@ setMethod("importPublicData", signature(source = "character", dataset = "charact

}

.importPublicData_F5 <- function(dataset = c("human", "mouse"), group = NULL, sample = NULL) {
dataset <- match.arg(dataset)
if (dataset == "human") {
if (! requireNamespace("BSgenome.Hsapiens.UCSC.hg19"))
stop ("This function requires the ", dQuote("BSgenome.Hsapiens.UCSC.hg19"), " package.")
FANTOM5humanSamples <- NULL
data("FANTOM5humanSamples", package = "CAGEr", envir = environment())
samples.info <- FANTOM5humanSamples
genome.name <- "BSgenome.Hsapiens.UCSC.hg19"
genome.obj <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
} else {
if (! requireNamespace("BSgenome.Mmusculus.UCSC.mm9"))
stop ("This function requires the ", dQuote("BSgenome.Mmusculus.UCSC.mm9"), " package.")
FANTOM5mouseSamples <- NULL
data("FANTOM5mouseSamples", envir = environment())
samples.info <- FANTOM5mouseSamples
genome.name <- "BSgenome.Mmusculus.UCSC.mm9"
genome.obj <- BSgenome.Mmusculus.UCSC.mm9::BSgenome.Mmusculus.UCSC.mm9
}
ce <- CAGEexp(genomeName = genome.name,
inputFiles = samples.info[samples.info$sample %in% sample,"data_url"],
inputFilesType = "bedScore",
sampleLabels = sample)
getCTSS(ce)
}

.importPublicData_ZF <- function(group = "development", sample = NULL) {
if (group != "development")
stop("Invalid group name! There is only one group in this dataset named 'development'.")
Expand Down Expand Up @@ -1001,3 +979,6 @@ setMethod("importPublicData", signature(source = "character", dataset = "charact
CTSStagCountSE(ce) <- ctssSE
ce
}

setMethod("importPublicData", signature(origin = "character", dataset = "character", sample = "character"),
.importPublicData)

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