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testCor.R

##test out my correlation function

library(ALL) data(ALL)

##GET BCR/ABL and NEG Bsub = grep("^B", as.character(ALL$BT)) Bcr = grep("^BCR", as.character(ALL$mol)) Bneg = grep("NEG", as.character(ALL$mol))

ALLs = ALL[, c(Bcr, intersect(Bsub, Bneg))]

##DROP unexpressed genes library(genefilter)

pF = pOverA(.25, 7)

whF = genefilter(ALLs, filterfun(pF))

ALLs2 = ALLs[whF,]

##find pairs library(hgu95av2)

lls = unlist(as.list(hgu95av2LOCUSID))

tab = table(lls)

data(hgu95av2LOCUSID2PROBE)

lp = as.list(hgu95av2LOCUSID2PROBE)

cts = listLen(lp)

have2 = cts==2

lp2 = lp[have2]

gN2 = geneNames(ALLs2)

haveBoth = sapply(lp2, function(x) if(all(!is.na(match(x, gN2))) ) TRUE else FALSE)

exprs2 = exprs(ALLs2)

##at least in this setting nothing good came of this

aa1 = sapply(lp3, function(x) cor(exprs2[x[1],], exprs2[x[2],]) )

aa2 = sapply(lp3, function(x) percentCor(exprs2[x[1],], exprs2[x[2],]))

aa3 = sapply(lp3, function(x) percentCor(exprs2[x[1],], exprs2[x[2],], 50))

aa4 = sapply(lp3, function(x) percentCor(exprs2[x[1],], exprs2[x[2],], method="spearman"))

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