Examples & Use Cases

The examples below show common FLiPPR workflows found in public use-cases.

Simple fold-change (LiP only)

from flippr import Study

study = Study(lip="/data/PXD/LiP_LFQ")
study.add_process("ctrl_v_treat", "CTRL", "TREAT", 3)
results = study.run()
res = results["ctrl_v_treat"]
# Inspect top peptides
print(res.peptide.head(10))

Fold-change with TrP normalization

If you have matched TrP data (no broad protease), provide it to Study and pass TrP args to add_process:

study = Study(lip="/data/PXD/LiP_LFQ", trp="/data/PXD/TrP_LFQ")
study.add_process("normed", "CTRL", "TREAT", 3, trp_ctrl="CTRL_TrP", trp_test="TREAT_TrP", trp_n_rep=3)
results = study.run()

Multiple-dose experiment

Add multiple processes to the same Study and run them together:

study.add_process("dose_lo", "CTRL", "DRUG_LO", 3, trp_ctrl="CTRL_TrP", trp_test="DRUG_TrP", trp_n_rep=3)
study.add_process("dose_hi", "CTRL", "DRUG_HI", 3, trp_ctrl="CTRL_TrP", trp_test="DRUG_TrP", trp_n_rep=3)
results = study.run()