plrs.series {plrs} | R Documentation

## Fit plrs models for a series of arrays.

### Description

The function fits `plrs` models for a series of arrays. Model selection and testing procedures may be applied.

### Usage

    plrs.series(expr, cghseg, cghcall=NULL,
    probloss = NULL, probnorm = NULL, probgain = NULL, probamp = NULL,
    control.model  = list(continuous = FALSE,
                          constr = TRUE,
                          constr.slopes = 2,
                          constr.intercepts = TRUE,
                          min.obs = 3,
                          discard.obs = TRUE),
    control.select = list(crit = ifelse(control.model$constr, "osaic","aic")),
    control.test   = list(testing = TRUE,
                          cb = FALSE,
                          alpha = 0.05),
    control.output = list(save.models = FALSE,
                          save.plots = FALSE,
                          plot.lin = FALSE,
                          type = "jpeg"))

### Arguments

`expr` | Either a matrix of expression profiles or an `ExpressionSet` object.
`cghseg` | Either a matrix of segmented copy number values or objects of class `cghSeg` or `cghCall`
`cghcall` | Matrix of called copy number
`probloss` | Matrix of call probabilities associated with state "loss". Default is `NULL`.
`probnorm` | Matrix of call probabilities associated with state "normal". Default is `NULL`.
`probgain` | Matrix of call probabilities associated with state "gain". Default is `NULL`.
`probamp` | Matrix of call probabilities associated with state "amplification". Default is `NULL`.
`control.model` | See details
`control.select` | See details
`control.test` | See details
`control.output` | See details

### Details

If DNA and mRNA input data are matrices, rows should correspond to genes and columns to arrays. Alternatively, expression data may be provided as an `ExpressionSet` object and aCGH data as `cghSeg` or `cghCall` objects. A `cghCall` object contain all data from the calling step, thus arguments `probloss`, `probnorm`, `probnorm` and `probamp` can be omitted. An object of class `cghSeg` does not contain such data so only simple linear models will be fitted.
`control.model` allows the user to specify the type of model that has to be fitted. This must be a `list` with one or more of the following components: `constr`, `constr.slopes`, `constr.intercepts`, `min.obs` and `discard.obs`. See functions `plrs` and `modify.conf` for more details.
`control.select` allows the user to specify whether model selection should be done and how. This must be a `list` with a component named `crit`. See function `plrs.select` for more details. If `control.select = NULL` then no model selection is done.
`control.output` allows the user to plot and save each `plrs` model. This must be a list with components:
`save.models`, a logical. This will create within the work directory a new directory named "plrsSeriesObjects" that will contain all objects.
`save.plots`, a logical. This will create within the work directory a new directory named "plrsSeriesPlots" that will contains all saved plots.
`plot.lin`, a logical. Whether the simple linear model should aslo be plotted.
`type`, a character. Format of file. To pass through function `savePlot`.

### Value

An object of class `plrs.series-class`

### Author(s)

Gwenael G.R. Leday g.g.r.leday@vu.nl

### Examples

    # Simulate data
    ngenes <- 10
    narray <- 48
    rna <- dnaseg <- dnacal <- matrix(NA, ngenes, narray)
    idx <- sample(1:4, ngenes, replace=TRUE, prob=rep(1/4,4))
    for(i in 1:ngenes){
    	Sim <- plrs.sim(n=narray, states=idx[i], sigma=0.5)
    	rna[i,] <- Sim$expr
    	dnaseg[i,] <- Sim$seg
    	dnacal[i,] <- Sim$cal
    }

    # Screening procedure with linear model
    series <- plrs.series(expr = rna, cghseg = dnaseg, cghcall = NULL, control.select = NULL)

    # Screening procedure with full plrs model
    series <- plrs.series(expr = rna, cghseg = dnaseg, cghcall = dnacal, control.select = NULL)

    # Model selection
    series <- plrs.series(expr = rna, cghseg = dnaseg, cghcall = dnacal)

[Package plrs version 1.27.0 Index]