normalize.loess: normalize.loess

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

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[,-1])

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.