dot-pickLoc: Select branches

Description Usage Arguments Value Author(s)

Description

.pickLoc selects two branches which meet the criteria specified by the arguments

Usage

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.pickLoc(tree = NULL, data = NULL, from.A = NULL, minTip.A = 0,
  maxTip.A = Inf, minTip.B = 0, maxTip.B = Inf, minPr.A = 0,
  maxPr.A = 1, ratio = 1)

Arguments

tree

A phylo object

data

A count table (a matrix or a data frame). It has tree leaves in rows and samples from different conditions in columns.

from.A

The branch node label of branch A. In simulation, we select two branches (A & B) to have differential abundance under different conditions. If from.A is specified, then branch A is fixed. If from.A is NULL, one can find a suitable branch which meets the criteria specified in minTip.A, maxTip.A, minPr.A and maxPr.A.

minTip.A

The minimum number of leaves in branch A

maxTip.A

The maximum number of leaves in branch A

minTip.B

The minimum number of leaves in branch B

maxTip.B

The maximum number of leaves in branch B

minPr.A

The minimum abundance proportion of leaves in branch A

maxPr.A

The maximum abundance proportion of leaves in branch A

ratio

The proportion ratio of branch B to branch A. This value is used to select branches(see Details). If there are no branches having exactly this ratio, the pair with the value closest to ratio would be selected.

Value

a data frame of one row

Author(s)

Ruizhu Huang


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