Check SUSILI Results

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Description

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

Usage

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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