From 48b5b7efd81b65c3bea131d50410aede26ed0686 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 28 Jan 2018 20:20:46 -0500
Subject: [PATCH] update
---
mhcflurry/class1_affinity_predictor.py | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 46e8d080..3eb2bfb6 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -629,7 +629,13 @@ class Class1AffinityPredictor(object):
sub_df.affinity, allele=allele, throw=throw)
return df.result.values
- def predict(self, peptides, alleles=None, allele=None, throw=True):
+ def predict(
+ self,
+ peptides,
+ alleles=None,
+ allele=None,
+ throw=True,
+ centrality_measure="robust_mean"):
"""
Predict nM binding affinities.
@@ -650,6 +656,9 @@ class Class1AffinityPredictor(object):
If True, a ValueError will be raised in the case of unsupported
alleles or peptide lengths. If False, a warning will be logged and
the predictions for the unsupported alleles or peptides will be NaN.
+ centrality_measure : string or callable
+ Measure of central tendency to use to combine predictions in the
+ ensemble. Options include: mean, median, robust_mean.
Returns
-------
@@ -661,6 +670,7 @@ class Class1AffinityPredictor(object):
allele=allele,
throw=throw,
include_percentile_ranks=False,
+ centrality_measure=centrality_measure,
)
return df.prediction.values
@@ -703,7 +713,7 @@ class Class1AffinityPredictor(object):
this will be ignored with a warning.
centrality_measure : string or callable
Measure of central tendency to use to combine predictions in the
- ensemble.
+ ensemble. Options include: mean, median, robust_mean.
Returns
-------
--
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