hyperrectangle_deviation_assessment: Calculation of deviation components

In jeitziner/TTMap: Two-Tier Mapper: a clustering tool based on topological data analysis

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");

jeitziner/TTMap documentation built on May 23, 2019, 4:24 p.m.