hyperrectangle_deviation_assessment {TTMap} | R Documentation

## Calculation of deviation components

### Description

`hyperrectangle_deviation_assessment` function calculates the hyperrectangle deviation assessment (HDA) that calculates the deviation components using `normal_hda2` which calculates the normal component of the test sample and `deviation_hda2` which calculates the deviation component.

### Usage

        hyperrectangle_deviation_assessment(x,
        k = dim(x$Normal.mat)[2], dataname,
        normalname,Org.directory = getwd())

### Arguments

`x` | output object given back by `control_adjustment`, list
`k` | A factor if not all the lines in the control group should be kept
`dataname` | the name of the project
`normalname` | A name for the corrected control files
`Org.directory` | where the outputs should be saved

### Details

The function performs the hyperrectangle deviation assessment (HDA)

### Value

Outputs

`Tdis.pcl` | The matrix of the deviation components for each test sample
`Tnorm.pcl` | The matrix of the normal components for each test sample
`NormalModel.pcl` | The normal model used

Values

`Dc.Dmat` | the deviation component matrix composed of the deviation components of all the samples in the test group
`m` | the values of the filter function per sample in the test group

### Author(s)

Rachel Jeitziner

### See Also

`control_adjustment`, `hyperrectangle_deviation_assessment`, `ttmap_sgn_genes`

### Examples

        ##a full example can be found in ttmap_sgn_genes
        ##--
        library(airway)
        data(airway)
        airway <- airway[rowSums(assay(airway))>80,]
        assay(airway) <- log(assay(airway)+1,2)
        ALPHA <- 1
        the_experiment <- TTMap::make_matrices(airway,
        seq_len(4), seq_len(4) + 4,
        rownames(airway), rownames(airway))
        TTMAP_part1prime <-TTMap::control_adjustment(
        normal.pcl = the_experiment$CTRL,
        tumor.pcl = the_experiment$TEST,
        normalname = "The_healthy_controls",
        dataname = "Effect_of_cancer",
        org.directory = tempdir(), e = 0, P = 1.1, B = 0);
        Kprime <- 4;
        TTMAP_part1_hda <-
        TTMap::hyperrectangle_deviation_assessment(x =
        TTMAP_part1prime,
        k = Kprime, dataname = "Effect_of_cancer",
        normalname = "The_healthy_controls");

[Package TTMap version 1.12.0 Index]