normalize.loess: normalize.loess

Description Usage Arguments Value Author(s) See Also Examples

View source: R/NormalizeBeta.R

Description

Loess normalization method.

Usage

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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",
  ...
)

Arguments

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 TRUE it takes the log2 of mat.

verbose

Logical. If TRUE displays current pair of chip being worked on.

span

Parameter to be passed the function loess

family.loess

Parameter to be passed the function loess. "gaussian" or "symmetric" are acceptable values for this parameter.

...

Any of the options of normalize.loess you would like to modify (described above).

Value

A matrix similar as mat.

Author(s)

Wubing Zhang

See Also

loess

NormalizeBeta

Examples

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file3 = file.path(system.file("extdata", package = "MAGeCKFlute"),
"testdata/mle.gene_summary.txt")
dd = ReadBeta(file3)
beta_loess = normalize.loess(dd[,c("dmso", "plx")])

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.