dot-doFC: Generate the fold change

Description Usage Arguments Value Author(s)

Description

.doFC generates fold changes for different scenarios

Usage

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.doFC(tree = NULL, data = NULL, scenario = "S1", branchA = NULL,
  branchB = NULL, ratio = 1, adjB = NULL, pct = 1)

Arguments

tree

A phylo object

data

The real data (count table)

scenario

Scenarios (“S1”, “S2”, “S3”)

branchA

The branch node label of branch A.

branchB

The branh node label of branch B.

ratio

The proportion ratio between branchB and branchA (B/A)

adjB

A numeric value between 0 and 1 (only for scenario is “S3”). Default is NULL. If NULL, branch A and branch B swap their proportions. If a numeric value, e.g. 0.1, then branch B decreases to its one tenth proportion and the decrease in branch B is added to branch A. For example, assume there are two experimental conditions (C1 & C2), branch A has 10 and branch B has 40 in C1. If adjB is set to 0.1, then in C2 branch B becomes 4 and branch A 46 so that the total proportion stays the same.

pct

The percentage (in number) of the leaves in branchA that will swap with branchB. The default is 1.

Value

numeric vector

Author(s)

Ruizhu Huang


markrobinsonuzh/treeAGG documentation built on May 26, 2019, 9:32 a.m.