inst/data_scripts/chin-2006/2-clean.r

In ramhiser/datamicroarray: Collection of Data Sets for Classification

# Chin et al. (2006) Breast Cancer Data Set
exprs_file <- file.path(temp_dir, ae_obj$processedFiles)
sdrf_file <- file.path(temp_dir, ae_obj$sdrf)

chin_x <- read.table(exprs_file, header=FALSE, sep="\t",
                     stringsAsFactors=FALSE)
subject_id <- as.character(chin_x[1, -1])
x <- unname(t(chin_x[-(1:2), -1]))

sdrf <- read.table(sdrf_file, header=TRUE, sep="\t",
                   stringsAsFactors=TRUE, comment.char="")
sdrf <- sdrf[sdrf[, 78] == "breastTumorExpression.txt", ]
sdrf <- sdrf[, c(35, 74)]
colnames(sdrf) <- c("class_label", "subject_id")

sdrf$subject_id <- as.character(sdrf$subject_id)

# We reorder the expressions and the class labels so that the subject ID's match
sdrf <- sdrf[order(sdrf$subject_id), ]
x <- x[order(subject_id), ]
y <- sdrf$class_label

class(x) <- 'numeric'

chin <- list(x=x, y=y)