Generate ph-site specific detailed file — artmsGeneratePhSiteExtended • artMS
Description: Generate extended detailed ph-site file, where every line is a ph site instead of a peptide. Therefore, if one peptide has multiple ph sites it will be breaking down in each of the sites. This file will help generate input files for tools as Phosfate or PHOTON

# Generate ph-site specific detailed file

Source: `R/analysisQuantifications.R`
`artmsGeneratePhSiteExtended.Rd`

Generate extended detailed ph-site file, where every line is a ph site instead of a peptide. Therefore, if one peptide has multiple ph sites it will be breaking down in each of the sites. This file will help generate input files for tools as Phosfate or PHOTON

    artmsGeneratePhSiteExtended(
      df,
      pathogen = "nopathogen",
      species,
      ptmType,
      output_name
    )

## Arguments

df | (data.frame) of log2fc and imputed values
pathogen | (char) Is there a pathogen in the dataset as well? Available pathogens are `tb` (Tuberculosis), `lpn` (Legionella). If it is not, then use `nopathogen` (default).
species | (char) Main organism (supported for now: `human` or `mouse`)
ptmType | (char) It must be a ptm-site quantification dataset. Either: yes: `ptmsites` (for site specific analysis), or `ptmph` (Jeff's script output evidence file).
output_name | (char) A output file name (extension `.txt` required)

## Value

(data.frame) extended version of the ph-site

## Examples

    if (FALSE) {
    artmsGeneratePhSiteExtended(df = dfobject,
                                 species = "mouse",
                                 ptmType = "ptmsites",
                                 output_name = log2fc_file)
    }