graph.edge.test {HapVLMC}R Documentation

Graph Edge Test

Description

Test case-control counts on edge versus totals. Edge is not tested if it does not participate in a merge (edges don't count towards merge if their count is < count.edge.threshold). Edge is not tested if total count for edge is < test.edge.threshold. Result is matrix, first column is level, second column is node, third column is p-value.

Usage

graph.edge.test(mygraph, count.edge.threshold = 2, test.edge.threshold = 50)

Arguments

mygraph A haplotype VLMC graph created with make.graph.
count.edge.threshold Edges are not counted if their count is less than this value.
test.edge.threshold Edges are not tested if the edge count is less than this value.

Value

A matrix, first column is level, second column is node, third column is edge, fourth column is p-value. One row per test.

Author(s)

Sharon Browning

References

S. Browning 2006 "Multilocus association mapping using variable length Markov chains".

See Also

alter.case, make.graph.


[Package HapVLMC version 2.0 Index]