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Last data update: 2014.03.03

R: Check SUSILI Results

check.Functions

R Documentation

Check SUSILI Results

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