Description Usage Arguments Examples
This function normalizes either raw data output from
BeadStudio or data of type MethyLumiSet
.
1 2 |
normfactors |
The output from
|
rawdata |
A |
featuredata |
A |
methylumidata |
A |
type |
One of either "raw" (default) or "methylumi" indicating the type of data supplied by the user. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ids <- seq(from = 10, to = 59)
n <- length(ids)
reds.s <- data.frame(matrix(rep(round(abs(rnorm(n, 4, 1))), 30), nrow=30))
names(reds.s) <- paste("X", ids, ".Signal_Red", sep = "")
greens.s <- data.frame(matrix(rep(round(abs(rnorm(n, 5, 2))), 30), nrow = 30))
names(greens.s) <- paste("X", ids, ".Signal_Grn", sep = "")
dat <- data.frame(reds.s, greens.s)
dat <- dat[,order(names(dat))]
indices <- sample(1:30, 30, replace = FALSE)
TargetID.s <- rep(NA, 30)
TargetID.s[indices[1:9]] <- "NORM_A"
TargetID.s[indices[10:18]] <- "NORM_T"
TargetID.s[indices[19:25]] <- "NORM_C"
TargetID.s[indices[25:30]] <- "NORM_G"
controldata.s <- data.frame(TargetID = TargetID.s, dat)
normfactors <- norm_factors(controldata=controldata.s, subjects=NULL)
ncpg <- 100
IlmnIDs.s <- paste("cg00", seq(1:ncpg), sep = "")
Infinium_Design_type.s <- sample(c("I", "II"), size=ncpg, replace = TRUE)
Color_Channel.s <- vector()
Color_Channel.s[Infinium_Design_type.s == "I"] <- sample(c("Red", "Grn"), size = length(Color_Channel.s[Infinium_Design_type.s == "I"]), replace = TRUE)
featuredata.s <- data.frame(IlmnIDs = IlmnIDs.s, Infinium_Design_Type = Infinium_Design_type.s, Color_Channel = Color_Channel.s)
signalA.s <- data.frame(matrix(rep(round(abs(rnorm(n, 4000, 2000))), ncpg), nrow=ncpg))
names(signalA.s) <- paste("X", ids, ".Signal_A", sep = "")
signalB.s <- data.frame(matrix(rep(round(abs(rnorm(n, 5000, 2000))), ncpg), nrow = ncpg))
names(signalB.s) <- paste("X", ids, ".Signal_B", sep = "")
dat <- data.frame(signalA.s, signalB.s)
mydata.s <- dat[,order(names(dat))]
newbetas <- normalize_asmn(normfactors=normfactors, rawdata=mydata.s, featuredata=featuredata.s, methylumidata = NULL, type = "raw")
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