artmsAnnotateSpecie {artMS} | R Documentation

## 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). Supported`tb` (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")

[Package artMS version 1.8.3 Index]