DELTA: Calculate DELTA score

In helloicyvodka/ggVITA: An R package for VIsualization and annotation of Tree Alignment.

Description

Calculate DELTA score

Usage

DELTA(treeS, treeT, cost, outfile = "./", method = "g", max_target = 1,
  test = 0, all = "F", prune = 1, DELTA.address = NULL)

Arguments

treeS:	TreeS file path.(required)
treeT:	TreeT file path.(required)
cost:	Cost file path. the cost file contains the score for different types of leaves.(required)
method:	l or g. g for global alignment; l for local alignment. default: g.
max_target:	target num for l, local alignment. default: 1
test:	testNum to calculate p-value. If testNum <=2, do not output p-value. default 0
outfile:	output file path. default: TreeS file path + l or g, based on -method
all:	T or F. output as much information as possible. default F;
prune:	pruneScore is the punish for pruning one leaf. default 1

helloicyvodka/ggVITA documentation built on May 28, 2019, 8:55 p.m.