normalize.loess {MAGeCKFlute} | R Documentation |
Loess normalization method.
normalize.loess( mat, subset = sample(1:(dim(mat)[1]), min(c(5000, nrow(mat)))), epsilon = 10^-2, maxit = 1, log.it = FALSE, verbose = TRUE, span = 2/3, family.loess = "symmetric", ... )
mat |
A matrix with columns containing the values of the chips to normalize. |
subset |
A subset of the data to fit a loess to. |
epsilon |
A tolerance value (supposed to be a small value - used as a stopping criterion). |
maxit |
Maximum number of iterations. |
log.it |
Logical. If |
verbose |
Logical. If |
span |
Parameter to be passed the function |
family.loess |
Parameter to be passed the function |
... |
Any of the options of normalize.loess you would like to modify (described above). |
A matrix similar as mat
.
Wubing Zhang
file3 = file.path(system.file("extdata", package = "MAGeCKFlute"), "testdata/mle.gene_summary.txt") dd = ReadBeta(file3) beta_loess = normalize.loess(dd[,c("dmso", "plx")])