testGroupIndependence {psichomics} | R Documentation

## Multiple independence tests between reference groups and list of groups

### Description

Test multiple contingency tables comprised by two groups (one reference group and another containing remaining elements) and provided groups.

### Usage

    testGroupIndependence(ref, groups, elements, pvalueAdjust = "BH")

### Arguments

`ref` | List of character: list of groups where each element contains the identifiers of respective elements
`groups` | List of characters: list of groups where each element contains the identifiers of respective elements
`elements` | Character: all available elements (if a data frame is given, its rownames will be used)
`pvalueAdjust` | Character: method used to adjust p-values (see Details)

### Details

The following methods for p-value adjustment are supported by using the respective string in the `pvalueAdjust` argument:

- `none`: Do not adjust p-values

- `BH`: Benjamini-Hochberg's method (false discovery rate)

- `BY`: Benjamini-Yekutieli's method (false discovery rate)

- `bonferroni`: Bonferroni correction (family-wise error rate)

- `holm`: Holm's method (family-wise error rate)

- `hochberg`: Hochberg's method (family-wise error rate)

- `hommel`: Hommel's method (family-wise error rate)

### Value

`multiGroupIndependenceTest` object, a data frame containing:

`attribute` | Name of the original groups compared against the reference groups
`table` | Contingency table used for testing
`pvalue` | Fisher's exact test's p-value

### See Also

`parseCategoricalGroups()` and `plotGroupIndependence()`

Other functions for data grouping: `createGroupByAttribute()`, `getGeneList()`, `getSampleFromSubject()`, `getSubjectFromSample()`, `groupPerElem()`, `plotGroupIndependence()`

### Examples

    elements <- paste("subjects", 1:10)
    ref      <- elements[5:10]
    groups   <- list(race=list(asian=elements[1:3],
                               white=elements[4:7],
                               black=elements[8:10]),
                     region=list(european=elements[c(4, 5, 9)],
                                 african=elements[c(6:8, 10)]))
    groupTesting <- testGroupIndependence(ref, groups, elements)
    # View(groupTesting)

[Package psichomics version 1.20.2 Index]