alluvial_enrichment_tests: alluvial_enrichment_tests

In langholee/XINA: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

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

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