R/utils.R

In Jfortin1/tcgaR: Interface in R for the TCGA Portal

#Tumor types range from 01 - 09, 
#normal types from 10 - 19 and 
#control samples from 20 - 29. 
.processBarcodes <- function(barcodes){
	tss <- substr(barcodes, 6, 7)
	participant <- substr(barcodes, 9, 12)
	sample.type <- substr(barcodes, 14, 15)
	sample.type <- as.numeric(as.character(sample.type))
	center <- substr(barcodes, 27, 28)
	vial <- substr(barcodes, 16, 16)
	portion <- substr(barcodes, 18,19)
	portion <- as.numeric(as.character(portion))
	sampleType <- structure(list(Code = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 
11L, 12L, 13L, 14L, 20L, 40L, 50L, 60L, 61L), Definition = structure(c(14L, 
18L, 13L, 16L, 1L, 11L, 2L, 10L, 12L, 3L, 19L, 5L, 9L, 4L, 8L, 
17L, 7L, 15L, 6L), .Label = c("Additional - New Primary", "Additional Metastatic", 
"Blood Derived Normal", "Bone Marrow Normal", "Buccal Cell Normal", 
"Cell Line Derived Xenograft Tissue", "Cell Lines", "Control Analyte", 
"EBV Immortalized Normal", "Human Tumor Original Cells", "Metastatic", 
"Primary Blood Derived Cancer - Bone Marrow", "Primary Blood Derived Cancer - Peripheral Blood", 
"Primary solid Tumor", "Primary Xenograft Tissue", "Recurrent Blood Derived Cancer - Bone Marrow", 
"Recurrent Blood Derived Cancer - Peripheral Blood", "Recurrent Solid Tumor", 
"Solid Tissue Normal"), class = "factor"), Short.Letter.Code = structure(c(14L, 
15L, 10L, 17L, 9L, 13L, 8L, 12L, 11L, 3L, 7L, 4L, 6L, 5L, 2L, 
16L, 1L, 19L, 18L), .Label = c("CELL", "CELLC", "NB", "NBC", 
"NBM", "NEBV", "NT", "TAM", "TAP", "TB", "TBM", "THOC", "TM", 
"TP", "TR", "TRB", "TRBM", "XCL", "XP"), class = "factor")), .Names = c("Code", 
"Definition", "Short.Letter.Code"), class = "data.frame", row.names = c(NA, 
-19L))
	#sampleType <- read.csv(file.path("/Users/Jean-Philippe/tcgaR/data/", "sampleType.csv"))
	sample.code <- sample.type
	sample.type <- as.character(sampleType$Definition[match(as.character(sample.type), sampleType$Code)])
	sample.id   <- paste(tss, participant, sample.code, vial,portion, sep="-")
	status <- sample.code
	status[status >= 1 & status <=9]  <- "Tumor"
	status[status >=10 & status <=19] <- "Normal"
	status[status >=20 & status <=29] <- "Control"

	data.frame(tss=tss, participant = participant, 
		sample.type = sample.type, 
		sample.code = sample.code, 
		status = status,
		center = center, 
		vial = vial,
		portion = portion,
		sample.id = sample.id
	)
}


.getTCGA.number <- function(cancer, platform = c("27k", "450k")){
	platform <- match.arg(platform)
	cancer <- tolower(cancer)
	filenames <- tcgaR:::.getIdatNames(cancer = cancer, platform = platform)
	n <- length(filenames[[1]])
	cat(paste0("[tcga.meth] ", n," samples have been found \n"))
}