Generate ph-site specific detailed file

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)
}