R/R2BASE.R

In SAGx: Statistical Analysis of the GeneChip

# Author PBG/28APR06
R2BASE <- function(context.data = clingen, sample.ids = AZID, expression.data = dats, annotation = annots, out = "u:/temp/temp.base"){
write(paste("BASEfile"), file = out)                                                                                                                                    
write(paste("section","assays",sep = "\t"),file = out, append = TRUE)                                                                                                                              
next.line = c(paste("count",ncol(expression.data)-1,sep = "\t"))
write.table(next.line, file = out, append = TRUE, quote = FALSE, row.names = FALSE, col.names = FALSE)  
next.line = paste(colnames(context.data), sep = "\t")
next.line =t(c(paste("columns",next.line,sep = "\t")))
write.table(next.line, file = out, append = TRUE, col.names = FALSE, row.names = FALSE, quote = FALSE)
next.line = c("%")
write(next.line,file = out, append = TRUE) 
write.table(context.data, file = out, sep = "\t", append = TRUE, quote = FALSE, row.names = FALSE, col.names = FALSE)
write("",sep = "\t",file = out, append = TRUE)    
write.table(data.frame("section","spots"), sep = "\t", file = out, append = TRUE, col.names = FALSE, row.names = FALSE, quote = FALSE)
write("", file = out, append = TRUE)
next.line = c(colnames(annotation))
next.line =t(c("columns",next.line,"assayData"))
write.table(next.line, sep = "\t", file = out, append = TRUE, col.names = FALSE, row.names = FALSE, quote = FALSE)
next.line = c(sample.ids)
next.line =t(c("assays",next.line))
write.table(next.line, file = out, se= "\t", append = TRUE, col.names = FALSE, row.names = FALSE, quote = FALSE)
expr = merge(annotation, expression.data, by.x = 1, by.y = 1)
write("%",file = out, append = TRUE)
write.table(expr, file = out, sep = "\t", append = TRUE, col.names = FALSE, row.names = FALSE, quote = FALSE)
}