artmsGeneratePhSiteExtended {artMS} | R Documentation

## Generate ph-site specific detailed file

### 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

### Usage

    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

    artmsGeneratePhSiteExtended(df = dfobject,
                                 species = "mouse",
                                 ptmType = "ptmsites",
                                 output_name = log2fc_file)

[Package artMS version 1.4.3 Index]