| 6dc7b945 |
|
| 6846d583 |
setMethod("Ns", signature(object="AssayData"),
|
| 3e4db4b1 |
function(object, ...){
|
| 0198a9ad |
batchnames <- sampleNames(object)
|
| 6dc7b945 |
N.AA <- assayDataElement(object, "N.AA")
N.AB <- assayDataElement(object, "N.AB")
N.BB <- assayDataElement(object, "N.BB")
|
| 3e4db4b1 |
res <- array(NA, dim=c(nrow(N.AA), 3, ncol(N.AA)))
|
| fda11070 |
dimnames(res)[[2]] <- c("AA", "AB", "BB")
dimnames(res)[[3]] <- batchnames
|
| 6dc7b945 |
res[, "AA", ] <- N.AA[,]
res[, "AB", ] <- N.AB[,]
res[, "BB", ] <- N.BB[,]
|
| fda11070 |
return(res)
|
| 6846d583 |
})
setMethod("corr", signature(object="AssayData"),
|
| d5b39e21 |
function(object, ...){
|
| 0198a9ad |
batchnames <- sampleNames(object)
|
| 6dc7b945 |
corrAA <- assayDataElement(object, "corrAA")
corrAB <- assayDataElement(object, "corrAB")
corrBB <- assayDataElement(object, "corrBB")
|
| 3e4db4b1 |
res <- array(NA, dim=c(nrow(corrAA), 3, ncol(corrAA)))
|
| fda11070 |
dimnames(res)[[2]] <- c("AA", "AB", "BB")
dimnames(res)[[3]] <- batchnames
|
| 6dc7b945 |
res[, "AA", ] <- corrAA[,]
res[, "AB", ] <- corrAB[,]
res[, "BB", ] <- corrBB[,]
|
| fda11070 |
return(res)
|
| 6846d583 |
})
setMethod("medians", signature(object="AssayData"),
|
| 3e4db4b1 |
function(object, ...){
|
| 0198a9ad |
batchnames <- sampleNames(object)
|
| 6dc7b945 |
medianA.AA <- assayDataElement(object, "medianA.AA")
medianA.AB <- assayDataElement(object, "medianA.AB")
medianA.BB <- assayDataElement(object, "medianA.BB")
medianB.AA <- assayDataElement(object, "medianB.AA")
medianB.AB <- assayDataElement(object, "medianB.AB")
medianB.BB <- assayDataElement(object, "medianB.BB")
|
| 3e4db4b1 |
res <- array(NA, dim=c(nrow(medianA.AA), 2, 3, ncol(medianA.AA)))
|
| fda11070 |
dimnames(res)[[2]] <- c("A", "B")
dimnames(res)[[3]] <- c("AA", "AB", "BB")
dimnames(res)[[4]] <- batchnames
|
| 6dc7b945 |
res[, "A", "AA", ] <- medianA.AA[,]
res[, "A", "AB", ] <- medianA.AB[,]
res[, "A", "BB", ] <- medianA.BB[,]
res[, "B", "AA", ] <- medianB.AA[,]
res[, "B", "AB", ] <- medianB.AB[,]
res[, "B", "BB", ] <- medianB.BB[,]
|
| fda11070 |
return(res)
|
| 6846d583 |
})
|
| fda11070 |
|
| 063b3d14 |
getMedians <- function(object){
medianA.AA <- assayDataElement(object, "medianA.AA")
medianA.AB <- assayDataElement(object, "medianA.AB")
medianA.BB <- assayDataElement(object, "medianA.BB")
medianB.AA <- assayDataElement(object, "medianB.AA")
medianB.AB <- assayDataElement(object, "medianB.AB")
medianB.BB <- assayDataElement(object, "medianB.BB")
list(A.AA=medianA.AA,
A.AB=medianA.AB,
A.BB=medianA.BB,
B.AA=medianB.AA,
B.AB=medianB.AB,
B.BB=medianB.BB)
}
|
| 3e4db4b1 |
setMethod("mads", signature(object="AssayData"),
function(object, ...){
|
| 0198a9ad |
batchnames <- sampleNames(object)
|
| 6dc7b945 |
madA.AA <- assayDataElement(object, "madA.AA")
madA.AB <- assayDataElement(object, "madA.AB")
madA.BB <- assayDataElement(object, "madA.BB")
madB.AA <- assayDataElement(object, "madB.AA")
madB.AB <- assayDataElement(object, "madB.AB")
madB.BB <- assayDataElement(object, "madB.BB")
|
| 3e4db4b1 |
res <- array(NA, dim=c(nrow(madA.AA), 2, 3, ncol(madA.AA)))
|
| fda11070 |
dimnames(res)[[2]] <- c("A", "B")
dimnames(res)[[3]] <- c("AA", "AB", "BB")
dimnames(res)[[4]] <- batchnames
|
| 6dc7b945 |
res[, "A", "AA", ] <- madA.AA[,]
res[, "A", "AB", ] <- madA.AB[,]
res[, "A", "BB", ] <- madA.BB[,]
res[, "B", "AA", ] <- madB.AA[,]
res[, "B", "AB", ] <- madB.AB[,]
res[, "B", "BB", ] <- madB.BB[,]
|
| fda11070 |
return(res)
|
| 6846d583 |
})
|
| fda11070 |
|
| 6846d583 |
setMethod("tau2", signature(object="AssayData"),
|
| 0198a9ad |
function(object, ...){
batchnames <- sampleNames(object)
|
| 6dc7b945 |
tau2A.AA <- assayDataElement(object, "tau2A.AA")
tau2A.BB <- assayDataElement(object, "tau2A.BB")
tau2B.AA <- assayDataElement(object, "tau2B.AA")
tau2B.BB <- assayDataElement(object, "tau2B.BB")
|
| 0198a9ad |
res <- array(NA, dim=c(nrow(tau2A.AA), 2, 2, ncol(tau2A.AA)))
dimnames(res)[[2]] <- c("A", "B")
dimnames(res)[[3]] <- c("AA", "BB")
dimnames(res)[[4]] <- batchnames
|
| 6dc7b945 |
res[, "A", "AA", ] <- tau2A.AA[,]
res[, "A", "BB", ] <- tau2A.BB[,]
res[, "B", "AA", ] <- tau2B.AA[,]
res[, "B", "BB", ] <- tau2B.BB[,]
|
| 0198a9ad |
return(res)
|
| 6846d583 |
})
|
