testStatPermutation {OmicsLonDA} | R Documentation

## Calculate testStat of each feature's time interval for all permutations

### Description

Calculate testStat of each feature's time interval for all permutations

### Usage

    testStatPermutation(perm)

### Arguments

`perm` | list has all the permutated models

### Value

a list of test statistic for each time interval for all all permutations

### References

Ahmed Metwally (ametwall@stanford.edu)

### Examples

    library(SummarizedExperiment)
    data("omicslonda_data_example")
    omicslonda_se_object_adjusted = adjustBaseline(
        se_object = omicslonda_data_example$omicslonda_se_object)
    omicslonda_test_object = omicslonda_se_object_adjusted[1,]
    se_object = omicslonda_test_object
    dt = data.frame(colData(se_object))
    dt$Count = as.vector(assay(se_object))
    Group = as.character(dt$Group)
    group.levels = sort(unique(Group))
    gr.1 = as.character(group.levels[1])
    gr.2 = as.character(group.levels[2])
    df = dt
    levels(df$Group) = c(levels(df$Group), "0", "1")
    df$Group[which(df$Group == gr.1)] = 0
    df$Group[which(df$Group == gr.2)] = 1
    group.0 = df[df$Group == 0, ]
    group.1 = df[df$Group == 1, ]
    points = seq(100, 130)
    perm  = permutationMC(formula = Count ~ Time, perm.dat = df, n.perm = 10,
                          fit.method = "ssgaussian", points = points,
                          parall = FALSE, prefix = tempfile())
    test.stat.prem = testStatPermutation(perm)

[Package OmicsLonDA version 1.8.0 Index]