fmm {PSEA} | R Documentation

## Full model matrix

### Description

Generates a model matrix containing (quantitative) independent variables and interaction regressors coding for group-specific effects for each of tthe quantitative variable.

### Usage

    fmm(v,d,int=TRUE)

### Arguments

`v` | n-by-m numeric matrix. Matrix containing m quantitative variables as columns (i.e. n is the number of samples).
`d` | n-by-o numeric matrix. Matrix containing o binary regressors (encoding o group-specific differences) as columns. n is the number of samples.
`int` | logical. If TRUE (default) an intercept is included as the first column of the full model matrix.

### Details

Quantitative variables are specified via the argument "v". Sample groups are specified using binary (i.e. 0,1) variables (argument "d"). The returned model matrix represents a linear model with "m" quantitative variables and "o" group effects (corresponding to "o"+1 sample groups).

Specifically, the columns of the full model matrix contain (in this order): an intercept (if "int" is TRUE), the quantitative variables in the same order as they are provided in the input, group-specific effects for each quantitative variable (encoded as interaction regressors and in the same order as the quantitative variable are provided in the input).

An interaction regressor corresponds a quantitative variable multiplied by a (group-specific) binary variable. It encodes the difference (for the particular variable) between a specific group and the reference group.

### Value

`fmm` | numeric matrix. The full model matrix. Its dimension is is n-by-(m*(o+1)+1) if int is TRUE and n-by-(m*(o+1)) if int is FALSE.

### Author(s)

Alexandre Kuhn alexandre.m.kuhn@gmail.com

### Examples

    ## Load example expression data (variable "expression")
    ## for 23 transcripts and 41 samples, and associated
    ## phenotype (i.e. group) information (variable "groups")
    data("example")

    ## The group data is encoded as a binary vector where
    ## 0s represent control samples (first 29 samples) and
    ## 1s represent disease samples (last 12 samples)
    groups

    ## Four cell population-specific reference signals
    ## (i.e. quantitative variable)
    neuron_probesets <- list(c("221805_at", "221801_x_at", "221916_at"),
                    "201313_at", "210040_at", "205737_at", "210432_s_at")
    neuron_reference <- marker(expression, neuron_probesets)

    astro_probesets <- list("203540_at",c("210068_s_at","210906_x_at"),
                    "201667_at")
    astro_reference <- marker(expression, astro_probesets)

    oligo_probesets <- list(c("211836_s_at","214650_x_at"),"216617_s_at",
                    "207659_s_at",c("207323_s_at","209072_at"))
    oligo_reference <- marker(expression, oligo_probesets)

    micro_probesets <- list("204192_at", "203416_at")
    micro_reference <- marker(expression, micro_probesets)

    ## Full model matrix with an intercept, 4 quantitative variables and
    ## group-specific (disease vs control) differences for the
    ## 4 quantitative variables
    fmm(cbind(neuron_reference, astro_reference, oligo_reference,
    	micro_reference), groups)

[Package PSEA version 1.21.1 Index]