omicslonda {OmicsLonDA} | R Documentation

## Omics Longitudinal Differential Analysis for one feature

### Description

Find significant time intervals of omic feature

### Usage

    omicslonda(se_object = NULL, n.perm = 500, fit.method = "ssgaussian",
      points = NULL, text = "FeatureName", parall = FALSE,
      pvalue.threshold = 0.05, adjust.method = "BH", time.unit = "days",
      ylabel = "Normalized Count", col = c("blue", "firebrick"),
      prefix = "Test")

### Arguments

`se_object` | SummarizedExperiment object contains omics count/level matrix and metadata contains (subject, time, group, and any any other covariates)
`n.perm` | number of permutations.
`fit.method` | fitting method (ssguassian).
`points` | points at which the prediction should happen.
`text` | Feature's name.
`parall` | boolean to indicate whether to use multicore.
`pvalue.threshold` | p-value threshold cutoff for identifing significant time intervals.
`adjust.method` | multiple testing correction method.
`time.unit` | time unit used in the Time vector (hours, days, weeks, months, etc.)
`ylabel` | text to be shown on the y-axis of all generated figures (default: "Normalized Count")
`col` | two color to be used for the two groups (eg., c("red", "blue")).
`prefix` | prefix to be used to create directory for the analysis results

### Value

a list of the significant time intervals for the tested feature, fitted model for each group, null distribution of the test statistic of the tested feature, and the original input data.

### 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,]
    points = seq(1, 500, length.out = 500)
    res = omicslonda(se_object = omicslonda_test_object, n.perm = 10,
                     fit.method = "ssgaussian", points = points, text = "Feature_1",
                     parall = FALSE, pvalue.threshold = 0.05,
                     adjust.method = "BH", time.unit = "days",
                     ylabel = "Normalized Count",
                     col = c("blue", "firebrick"), prefix = tempfile())

[Package OmicsLonDA version 1.0.0 Index]