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dibakar ray
▴
40
@dibakar-ray-413
Last seen 10.1 years ago
Sorry to bother you people with my silly questions.
Following codes are from Lab5 and Lab6 pdf files available at the web
site.
I could understand the following code.
===================================
> data(golubTrain)
> X <- exprs(golubTrain)
> X[X < 100] <- 100
> X[X > 16000] <- 16000
> mmfilt <- function(r = 5, d = 500, na.rm = TRUE) {
+ function(x) {
+ minval <- min(x, na.rm = na.rm)
+ maxval <- max(x, na.rm = na.rm)
+ (maxval/minval > r) && (maxval - minval > d)
+ }
+ }
> mmfun <- mmfilt()
> ffun <- filterfun(mmfun)
> sub <- genefilter(X, ffun)
> sum(sub)
[1] 3051
> X <- X[sub, ]
> X <- log2(X)
==========================
But I am unable to understand this portion -
============= ===================
> golubTrainSub <- golubTrain[sub, ]
> golubTrainSub@exprs <- X
> Y <- golubTrainSub$ALL.AML
#I understand the following line
> Y <- paste(golubTrain$ALL.AML, golubTrain$T.B.cell)
# DO NOT UNDERSTAND THE FOLLOWING ONE.
> Y <- sub("NA", "", Y)
========================================================
From Lab6 Code, the following is OK
================================
> data(golubTrain)
> data(golubMerge)
> data(golubTest)
> gTrn <- GolubTrans(golubTrain)
> gTest <- GolubTrans(golubTest)
> gMerge <- GolubTrans(golubMerge)
> mmfun <- mmfilt()
> ffun <- filterfun(mmfun)
> sub <- genefilter(gTrn, ffun)
But why we need to set the following element False?
> sub[c(2401, 3398, 4168)] <- FALSE
Thanks
Dibakar Ray
