add.model: Object constructor for binary predictors
In FSAtools: Fragment Analysis and Capillary Sequencing Tool Kit

add.model

R Documentation

Object constructor for binary predictors

Description

This function aggregates the data required to predict class in classify.

Usage

  add.model(x, model, groupMeans, groupSDs, groupNames, groupColors, threshold,
    geneNames, geneTs, geneMs)

Arguments

`x`	An object of class `fsa` to which add a model.
`model`	A `list` aggregating the model parameters. Can be provided instead of the argument vectors below individually.
`groupMeans`	Numeric vector of length 2, the means of the scores in each group as computed on a training series. If `model` is provided, this vector will be used instead.
`groupSDs`	Numeric vector of length 2, the standard deviations of the scores in each group as computed on a training series. If `model` is provided, this vector will be used instead.
`groupNames`	Character vector of length 2, the names of the group described in `groupMeans`, `groupSDs` and `groupColors`. If `model` is provided, this vector will be used instead.
`groupColors`	Character vector of length 2, the colors to use to plot each group (see `par` for allowed values). If `model` is provided, this vector will be used instead.
`threshold`	Single numeric vector, the confidence threshold to use for prediction (a call will be made only if it is at least at this level of certainty). If `model` is provided, this vector will be used instead.
`geneNames`	Character vector, the names of the genes whose expression is to be used. If `model` is provided, this vector will be used instead.
`geneTs`	Numeric vector, for each gene in `geneNames`, the statistic of a `t.test` comparing its expression between the two groups in a training series. If `model` is provided, this vector will be used instead.
`geneMs`	Numeric vector, for each gene in `geneNames`, the mean expression in the whole training series. If `model` is provided, this vector will be used instead.

Value

Returns an S3 object of class fsaModel.

Author(s)

Sylvain Mareschal

Examples

  # Example FSA file provided
  fsa <- read.fsa(system.file("extdata/fsa_GEP/A5918.fsa", package="FSAtools"))
  
  # Add model from design file
  design <- designFile(system.file("extdata/design_GEP.conf", package="FSAtools"))
  fsa <- add.model(fsa, model=design$GLOBALS$MODEL)
  
  # Observe model
  print(attr(fsa, "model"))
  plot(attr(fsa, "model"))

FSAtools documentation built on Aug. 19, 2023, 1:06 a.m.