normalize.loess {MAGeCKFlute} | R Documentation

## normalize.loess

### Description

Loess normalization method.

### Usage

    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

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

[Package MAGeCKFlute version 1.14.0 Index]