check.Function: Check SUSILI Results

In megaptera: MEGAPhylogeny Techniques in R

Description

This set of functions helps to check progress and consistency of a megaptera project.

Usage

check.NameChanges(conn, order.by = "spec")
check.Species(conn, spec, gene)
check.Markers(conn, subset, outgroup, colname = "blocks", plot = TRUE)
check.Coverage(conn, pool.markers = TRUE)
check.Clades(phy, tax)

Arguments

conn	a database connection object.
spec	character string giving the name of a species
gene	character string giving the name of a genetic marker
subset	character string giving the names of a subset of species
outgroup	character string giving the name(s) of outgroup species
order.by	a character string giving the column name that is used for ordering the output table
colname	character string: gb, sel, or blocks.
plot	logical
pool.markers	logical
phy	an object of class phylo
tax	a data frame containing a taxonomic classification

Value

a data frame

Author(s)

Christoph Heibl

References

http://www.ncbi.nlm.nih.gov/taxonomy

megaptera documentation built on Jan. 15, 2017, 11:19 p.m.