tableSpecies: Tables the species in xml file

In fischuu/hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

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)

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.

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.

Value

A table with the species from the XML file

Author(s)

Daniel Fischer

Examples

## Not run: 
tableSpecies(xmls)
pigHits <- tableSpecies(xmls, species="Sus scrofa", locations = TRUE)

## End(Not run)

fischuu/hoardeR documentation built on April 13, 2024, 1:20 p.m.