Basic usage
Let’s quickly demonstrate how to use this package.
Installation
Use pip to install xiFDR from PyPi:
$ pip install xifdr
If you use a free threaded python version install with the nogil option:
$ pip install 'xifdr[nogil]'
Input format
The full FDR calculation and the boosting methods both support polars or pandas DataFrames. The following column names play special roles in the FDR calculcation:
column name |
required? |
function |
|---|---|---|
score |
yes |
score for FDR calculation |
sequence_p1 |
yes |
sequence for peptide 1 including modifications |
sequence_p2 |
yes |
sequence for peptide 2 including modifications |
start_pos_p1 |
yes |
position(s) of peptide 1 in the according protein(s) |
start_pos_p2 |
yes |
position(s) of peptide 2 in the according protein(s) |
link_pos_p1 |
yes |
link position in the sequence of peptide 1 |
link_pos_p2 |
yes |
link position in the sequence of peptide 2 |
charge |
yes |
precursor charge |
protein_p1 |
yes |
protein(s) related to peptide 1 |
protein_p2 |
yes |
protein(s) related to peptide 2 |
decoy_p1 |
yes |
decoy indicator for peptide 1 |
decoy_p2 |
yes |
decoy indicator for peptide 2 |
fdr_group |
no |
groups for crosslink FDR calculation |
coverage_p1 |
no |
fragment coverage of peptide 1 (default: 0.5) |
coverage_p2 |
no |
fragment coverage of peptide 2 (default: 0.5) |
Running a full multi-level FDR
TODO
Running a boosted multi-level FDR
TODO