Description Usage Arguments Value Examples
Using either raw data from BeadStudio or
MethyLumiSet
data, this function creates
normalization factors using either all subjects' means or a
subset.
1 2 |
controldata |
A |
subjects |
Optional. User can specify the index or names of a given subject or range of subjects to use in the creation of the normalization factors as oppposed to using all the samples. |
methylumidata |
A |
type |
One of either "raw" (default) or "methylumi" indicating the type of data supplied by the user. |
A list of length two containing the normalization factors for each subject in each color channel.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | 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, type = "raw")
normfactors <- norm_factors(controldata=controldata.s, subjects=1, type = "raw")
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