calcul_e {TTMap} | R Documentation

## Calculation of the value of epsilon

### Description

Calculation of the value of epsilon

### Usage

        calcul_e(dd5, pvalcutoff = 0.95, tt1, alpha = 1, S =
        colnames(tt1$Normal.mat))
        calcul_e_single(dd5, pvalcutoff = 0.95, tt1, alpha = 1, S =
        colnames(tt1$Normal.mat))

### Arguments

`dd5` | distance matrix as created by `generate_mismatch_distance`
`pvalcutoff` | cutoff of 0.05 percent (default) or less
`tt1` | output of `control_adjustment`
`alpha` | a cutoff value for the FC between the group of control and the disease group
`S` | subset of columns to be considered

### Value

`al` | number representing the cutoff to choose for the relatedness with dd5

### Author(s)

Rachel Jeitziner

### See Also

`control_adjustment`, `hyperrectangle_deviation_assessment`, `ttmap_sgn_genes`, `generate_mismatch_distance`

### Examples

        ##--
        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");
        annot <- c(paste(colnames(
        the_experiment$TEST[,-(seq_len(3))]), "Dis", sep = "."),
        paste(colnames(the_experiment$CTRL[,
        -seq_len(3)]), "Dis", sep = "."))
        dd5_sgn_only <-TTMap::generate_mismatch_distance(
        TTMAP_part1_hda,
        select=rownames(TTMAP_part1_hda$Dc.Dmat), alpha = ALPHA)
        e <- TTMap::calcul_e(dd5_sgn_only, 0.95, TTMAP_part1prime, 1)

[Package TTMap version 1.12.0 Index]