alluvial_enrichment_tests {XINA} | R Documentation |
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.
alluvial_enrichment_tests(count_table, c1, c2, non_cluster = 0, test_type = "fisher")
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 |
P-value of comigration enrichment test and 2x2 table information