ruvms: Remove unwanted variation in mass-spectrometry data
In Mengbo-Li/ruvms: Removing Unwanted Variations in Mass-Spectrometry Data.

ruvms

R Documentation

Remove unwanted variation in mass-spectrometry data

Description

The 'ruvms' function performs an 'ruv::RUVIII' like normalisation on mass-spectrometry data while allowing missing values (NAs) in input data.

Usage

ruvms(
  Y,
  M,
  ctl,
  k1 = 0,
  lambda = 1e-05,
  standardise = TRUE,
  delta = NULL,
  eta = NULL,
  include.intercept = TRUE,
  average = FALSE,
  return.info = FALSE,
  inputcheck = FALSE
)

Arguments

`Y`	The data. An m-by-n matrix, where m is the number of observations and n is the number of measurements.
`M`	The replication structure matrix. See `ruv::RUVIII` for details.
`ctl`	A logical vector of length n indicating the negative control measurements (peptides, proteins or metabolites).
`k1`	Tuning parameter. Default is 0.
`lambda`	Tuning parameter. Default is 1e-5, only needed when `standardise` is `FALSE`.
`eta`	Column-wise (e.g., protein-wise) covariates. See `ruv::RUVI` for more.
`include.intercept`	Logical. See `ruv::RUVI` for more.
`average`	Logical, whether to return averaged replicates after normalisation.
`return.info`	Logical. If `FALSE`, only the adjusted data matrix is returned. If `TRUE`, additional information is returned (see below).
`input.check`	Logical. A basic sanity check on the inputs.

Value

If input.check = FASLE, the normalised data matrix is returned. Otherwise a list is returned which contains

`newY`					The normalised data matrix.
`di`					Eigenvalues of the N matrix.
`hi`					hi values in the generalised averging operator.
`delta`					The delta tuning parameter.
`lambda`					The lambda tuning parameter.