artmsAnnotateSpecie: Adding a column with the species name

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

Adding a column with the species name

Description

Adding the species name to every protein. This makes more sense if there are more than one species in the dataset, which must be specified in the pathogen option. Influenza is a special case that it does not need to be specified, as far as the proteins were originally annotated as INFLUENZAGENE_STRAIN (strains covered H1N1, H3N2, H5N1), as for example, NS1_H1N1

Usage

artmsAnnotateSpecie(df, pathogen = "nopathogen", species)

Arguments

df	(data.frame) with a Protein column (of uniprot ids)
pathogen	(char) Is there a pathogen in the dataset as well? if it does not, then use pathogen = nopathogen (default). Supportedtb (Tuberculosis), lpn (Legionella)
species	(char) Host organism (supported for now: human or mouse)

Value

(data.frame) The same data.frame but with an extra column specifying the species

Examples

# Adding a new column with the main species of the data. Easy.
# But the main functionality is to add both the host-species and a pathogen,
# which is not illustrated in this example
data_with_specie <- artmsAnnotateSpecie(df = artms_data_ph_msstats_results,
                                         species = "human")

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.