alluvial_enrichment_tests {XINA} | R Documentation

## alluvial_enrichment_tests

### Description

Fisher's exact test to calculate the significance over all comigrations. The following 2x2 table was used to calculate p-value from Fisher's exact test. To evaluate significance of comigrated proteins from cluster #1 in control to cluster #2 in test condition,

| cluster #1 in control | other clusters in control
cluster #2 in test | 65 (TP) | 175 (FP)
other clusters in test | 35 (FN) | 979 (TN)

'alluvial_enrichment_tests' also provides another statistical methods including Hypergeometric test and Chi-square test.

### Usage

    alluvial_enrichment_tests(count_table, c1, c2, non_cluster = 0,
      test_type = "fisher")

### Arguments

`count_table` | A data frame generated by using count.
`c1` | A selected cluster in the first condition.
`c2` | A selected cluster in the second condition.
`non_cluster` | The cluster number for proteins that were not detected in a specific sample. Default is 0.
`test_type` | Enrichment test type. 'fisher' = Fisher's exact test, 'hyper' = Hypergeometric test, 'chisq' = Chi-square test

### Value

P-value of comigration enrichment test and 2x2 table information

[Package XINA version 1.12.0 Index]