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 1.9.0 Index]