bara_fit: Creates a BARA fit object

Description Usage Arguments Value

Description

The function is applied to the training set and returns a BaraFit object that can be used to adjust batch effects in subsequently acquired test sets.

Usage

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bara_fit(x, ref, ndim = NULL, loss = NULL, scale_var = FALSE,
  verbose = TRUE)

Arguments

x

Matrix, the training data set with samples in rows.

ref

Numeric vector, index of the reference samples.

ndim

Integer, describes the number of SVD dimensions to retain. If NULL, the all possible dimensions are calculated.

loss

Numeric between 0 and 1. Describes the maximum amount of variance that can be lost during compression.

scale_var

Logical, should the variance be scaled? Default is FALSE.

verbose

Logical, should runtime messages be printed? Default is TRUE.

Value

An object of class BaraFit.

x

Compressed and reconstructed training data set. Can be used to define subsequent prediction model.

ref

Index of reference samples.

means

Mean values of the columns of the input matrix x.

sds

Standard deviations of the columns of the input matrix x.

right_vectors

Right singular vectors of the input matrix x.

ref_means

Mean values of the reference samples in the compressed data space.

call

Function call.


robingradin/bara documentation built on May 9, 2019, 2:24 a.m.