hoardeR (version 0.10)

tableSpecies: Tables the species in xml file

Description

Tables the species in xml file

Usage

tableSpecies(xml, species=NULL, type="chr", minOutput=TRUE, exclude="",
               locations=FALSE)

Value

A table with the species from the XML file

Arguments

xml

The xml file.

species

Restrict species to a certain set.

type

Filter option.

minOutput

Logical, should the output be minimal.

exclude

Names of species to exclude.

locations

Logical, shall the hit locations be given as well.

Author

Daniel Fischer

Details

Function provides a table of identified species. This table can e.g. be put into the barplot function to visualize the findings.

Further, if the option locations is set to TRUE the function not only tables the species, but also the individual locations of the hits. This output is required for the further steps. Hence, this function plays a important role in the identification pipeline.

Be default the option type="chr" is set so that only hits in species will full genomes will be reported. Further, the species names are intersected with the species data frame and only those that appear there are reported.

Examples

if (FALSE) {
tableSpecies(xmls)
pigHits <- tableSpecies(xmls, species="Sus scrofa", locations = TRUE)
}