alluvial_enrichment_tests: alluvial_enrichment_tests

Description Usage Arguments Value

View source: R/coregulstions.R

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

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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


langholee/XINA documentation built on March 17, 2020, 5:23 p.m.