IWTomicsTest {IWTomics} | R Documentation

## Interval-Wise Testing

### Description

The function implements the Interval-Wise Testing for omics data (both one sample and two sample tests), an extended version of the Interval-Wise Testing for functional data presented in Pini and Vantini (2017). This inferential procedure tests for differences in feature measurements between two region datasets (two sample test) or between a region dataset and a reference curve (one sample test).

### Usage

    IWTomicsTest(regionsFeatures,
      id_region1=idRegions(regionsFeatures)[1], id_region2=NULL,
      id_features_subset=idFeatures(regionsFeatures), mu=0,
      statistics="mean", probs=0.5, max_scale=NULL, paired=FALSE, B=1000)

### Arguments

`regionsFeatures` | `"IWTomicsData"` object.
`id_region1` | identifier(s) of the region dataset(s) to be tested. If a vector is provided, a test will be performed for each element of the vector.
`id_region2` | identifier(s) of the region dataset(s) to be tested for two sample test. If `NULL` or empty string, one sample test is performed.
`id_features_subset` | vector with the identifiers of the features to be tested.
`mu` | the reference curve (center of symmetry) under the null hypothesis in one sample test, or the difference between the two populations in two sample test. Can be either a constant (the same constant curve for all features), a vector of constants (a constant curve for each feature), or a list of vectors containing its measurements for each feature (on the same grid as the features). Default `mu=0`.
`statistics` | test statistics to be used in the test. Possible test statistics are `"mean"`, `"median"`, `"variance"` and `"quantile"`.
`probs` | probabilities corresponding to the quantiles in test statistics `"quantile"`. If multiple quantiles are selected, the test statistics is the sum of the statistics on the different quantiles.
`max_scale` | the maximum interval length to be used for the p-value adjustment, i.e. the maximum number of consecutive windows to be employed (can range from 1 to the maximum number of consecutive measurements present for the feature tested). Can be either a scalar (the same length for all features) or a vector (a length for each feature) or a list of vectors (a vector for each test). If `NULL`, the maximum possible interval length is used.
`paired` | if `TRUE`, a paired (two sample) test is performed.
`B` | number of iterations of the MC algorithm to evaluate the p-values of the permutation tests. If B is greater than the number of possible permutations, exact p-values are computed.

### Value

The function `IWTomicsTest` returns an object of class `"IWTomicsData"` containing the region datasets and feature datasets tested, and with the test input and result in the optional slot `test`.

### Note

In this implementation of Interval-Wise Testing, the smallest scale considered corresponds to the measurement resolution, i.e. the univariate (unadjusted) tests are done on each measurement window. To change the smallest scale considered the method `smooth` can be employed.

If the region alignment is `"scale"`, the function `smooth` must be used before applying the Interval-Wise Testing in order to measure the features over the grid in all the regions.

### Author(s)

Marzia A Cremona, Alessia Pini, Francesca Chiaromonte, Simone Vantini

### References

A Pini and S Vantini (2017). Interval-Wise Testing for functional data. Journal of Nonparametric Statistics.

### See Also

`IWTomicsData` for `"IWTomicsData"` class, constructors, accessors and methods; `plot` method to plot `"IWTomicsData"` objects; `smooth` to smooth curves before testing; `plotTest` to plot the test results; `plotSummary` to draw a summary plot of the test results.

### Examples

    ## -------------------------------------------------------------------------------------------
    ## -------------------------------------------------------------------------------------------
    ## EXAMPLE ON REAL DATA
    ## -------------------------------------------------------------------------------------------
    ## -------------------------------------------------------------------------------------------
    ## ETn Recombination hotspots data
    ## Two region datasets:
    ## ETns fixed 64-kb flanking regions and 64-kb control regions in mouse
    ## One feature measured in 1-kb windows:
    ## Recombination hotspots content
    ## ?ETn_example for details on the dataset
    data(ETn_example)
    ETn_example

    ## Two sample test to compare recombination hotspots
    ## in ETn regions vs control regions
    ETn_test=IWTomicsTest(ETn_example,
                         id_region1='ETn_fixed',id_region2='Control')
    ## Adjusted p-value
    adjusted_pval(ETn_test)

    ## Adjusted p-value lowering the scale of the test
    adjusted_pval(ETn_test,scale_threshold=10)

    ## -------------------------------------------------------------------------------------------
    ## -------------------------------------------------------------------------------------------
    ## EXAMPLE ON SIMULATED DATA
    ## -------------------------------------------------------------------------------------------
    ## -------------------------------------------------------------------------------------------

    ## -------------------------------------------------------------------------------------------
    ## -------------------------------------------------------------------------------------------
    ## CURVE ALIGNMENT CENTER
    ## -------------------------------------------------------------------------------------------
    ## -------------------------------------------------------------------------------------------
    data(regionsFeatures_center)

    ## One sample test for 'control' regions and feature 'ftr1'
    regionsFeatures_test=IWTomicsTest(regionsFeatures_center,
                                      id_region1='control',id_features_subset='ftr1')
    adjusted_pval(regionsFeatures_test)

    ## Plotting the results of the one sample test
    plotTest(regionsFeatures_test,col=5)

    ## Two sample test for 'elem1', 'elem2' and 'elem3' vs 'control' regions and feature 'ftr1'
    regionsFeatures_test=IWTomicsTest(regionsFeatures_center,
                                      id_region1=c('elem1','elem2','elem3'),
                                      id_region2=c('control','control','control'),
                                      id_features_subset='ftr1')
    adjusted_pval(regionsFeatures_test)

    ## Plotting the results of the two sample test
    plotTest(regionsFeatures_test)

    ## Summary plot of the two sample test
    ## x11(10,5)
    plotSummary(regionsFeatures_test,groupby='feature',align_lab='Center')

    #############################################################################################
    ## Not run:
    #############################################################################################
    ## Using 'quantile' test statistics with multiple quantiles
    regionsFeatures_test=IWTomicsTest(regionsFeatures_center,
                                      id_region1=c('elem1','elem2','elem3'),
                                      id_region2=c('control','control','control'),
                                      id_features_subset='ftr1',
                                      statistics='quantile',probs=c(0.25,0.75))
    adjusted_pval(regionsFeatures_test)

    ## Plotting the results of the two sample test
    plotTest(regionsFeatures_test)

    ## Summary plot of the two sample test
    ## x11(10,5)
    plotSummary(regionsFeatures_test,groupby='feature',align_lab='Center')
    #############################################################################################
    ## End(Not run)
    #############################################################################################

    ## -------------------------------------------------------------------------------------------
    ## -------------------------------------------------------------------------------------------
    ## CURVE ALIGNMENT SCALE
    ## -------------------------------------------------------------------------------------------
    ## -------------------------------------------------------------------------------------------
    data(regionsFeatures_scale)

    ## Smooth the curves to have measurements on the same grid
    regionsFeatures_smooth=smooth(regionsFeatures_scale,type='locpoly',scale_grid=30)

    ## Two sample test for 'elem1', 'elem2' and 'elem3' vs 'control' regions and feature 'ftr2'
    regionsFeatures_test=IWTomicsTest(regionsFeatures_smooth,
                                      id_region1=c('elem1','elem2','elem3'),
                                      id_region2=c('control','control','control'),
                                      id_features_subset='ftr2')
    adjusted_pval(regionsFeatures_test)

    ## Plotting the results of the two sample test
    plotTest(regionsFeatures_test)

    ## Summary plot of the two sample test
    ## x11(10,5)
    plotSummary(regionsFeatures_test,groupby='feature')

[Package IWTomics version 1.16.0 Index]