psite_annotation.addPSPAnnotations

psite_annotation.addPSPAnnotations(df, phosphoSitePlusFile, organism='human')

Annotate pandas dataframe with number of high and low-throughput studies according to PhosphositePlus.

Adds the following annotation columns to dataframe:

  • LT_LIT = number of low-throughput studies

  • MS_LIT = number of high-throughput Mass Spec studies

  • MS_CST = number of high-throughput Mass Spec studies by CellSignalingTechnologies

Example

df = pa.addPeptideAndPsitePositions(df, pa.pspFastaFile, pspInput = True)
df = pa.addPSPAnnotations(df, pa.pspAnnotationFile)
Required columns:

Site positions

Parameters:

  • df (DataFrame) – pandas dataframe with ‘Site positions’ column

  • phosphoSitePlusFile (str) – tab separated file with PhosphositePlus annotations

Returns:

annotated dataframe

Return type:

pd.DataFrame