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Lukas Käll percolator

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  • Science for Life Laboratory, KTH
  • Stockholm, Sweden
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percolator / gist:3dddda19353612212f34d8305751f061
Created September 19, 2018 12:14
pi_0 estimation
def bootstrap(invec):
idx = npr.randint(0, len(invec), len(invec))
return [invec[i] for i in idx]
def estimatePi0(p, numBoot=100, numLambda=100, maxLambda=0.95):
p.sort()
n=len(p)
lambdas=np.linspace(maxLambda/numLambda,maxLambda,numLambda)
Wls=np.array([n-np.argmax(p>=l) for l in lambdas])
pi0s=np.array([Wls[i] / (n * (1 - lambdas[i])) for i in range(numLambda)])
@percolator
percolator / qvalues.py
Last active November 25, 2018 09:20
Snippet generating q values from p values
def bootstrap(invec):
idx = npr.randint(0, len(invec), len(invec))
return [invec[i] for i in idx]
def estimatePi0(p, numBoot=100, numLambda=100, maxLambda=0.95):
p.sort()
n=len(p)
lambdas=np.linspace(maxLambda/numLambda,maxLambda,numLambda)
Wls=np.array([n-np.argmax(p>=l) for l in lambdas])
pi0s=np.array([Wls[i] / (n * (1 - lambdas[i])) for i in range(numLambda)])
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percolator / Exe1.ipynb
Created October 25, 2017 09:32
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percolator / pam250.py
Created October 11, 2017 16:22
PAM250 = {
'A': {'A': 2, 'C': -2, 'D': 0, 'E': 0, 'F': -3, 'G': 1, 'H': -1, 'I': -1, 'K': -1, 'L': -2, 'M': -1, 'N': 0, 'P': 1, 'Q': 0, 'R': -2, 'S': 1, 'T': 1, 'V': 0, 'W': -6, 'Y': -3},
'C': {'A': -2, 'C': 12, 'D': -5, 'E':-5, 'F': -4, 'G': -3, 'H': -3, 'I': -2, 'K': -5, 'L': -6, 'M': -5, 'N': -4, 'P': -3, 'Q': -5, 'R': -4, 'S': 0, 'T': -2, 'V': -2, 'W': -8, 'Y': 0},
'D': {'A': 0, 'C': -5, 'D': 4, 'E': 3, 'F': -6, 'G': 1, 'H': 1, 'I': -2, 'K': 0, 'L': -4, 'M': -3, 'N': 2, 'P': -1, 'Q': 2, 'R': -1, 'S': 0, 'T': 0, 'V': -2, 'W': -7, 'Y': -4},
'E': {'A': 0, 'C': -5, 'D': 3, 'E': 4, 'F': -5, 'G': 0, 'H': 1, 'I': -2, 'K': 0, 'L': -3, 'M': -2, 'N': 1, 'P': -1, 'Q': 2, 'R': -1, 'S': 0, 'T': 0, 'V': -2, 'W': -7, 'Y': -4},
'F': {'A': -3, 'C': -4, 'D': -6, 'E':-5, 'F': 9, 'G': -5, 'H': -2, 'I': 1, 'K': -5, 'L': 2, 'M': 0, 'N': -3, 'P': -5, 'Q': -5, 'R': -4, 'S': -3, 'T': -3, 'V': -1, 'W': 0, 'Y': 7},
'G': {'A': 1, 'C': -3, 'D': 1, 'E': 0, 'F': -5, 'G': 5, 'H': -2, 'I': -3, 'K': -
@percolator
percolator / generate_expression_data.py
Last active October 20, 2017 13:00
A sniplet generating data simulating a high throughput expression analysis experiment
import numpy as np
import numpy.random as npr
import pandas as pd
def generate_expression_data(n_analytes=100, n_samples=2, n_replicates=3, p_regulated=0.2, mean_offset=3.0, var=0.2, diff_var=2.0):
# Here we follow a convension, The first sample is the reference i.e. have all label 1
labels = npr.binomial(1, p_regulated, (n_analytes,n_samples-1))
template = np.hstack((np.zeros((n_analytes,1)),labels))
# We expand the template labels into several replicates
@percolator
percolator / index.html
Last active September 8, 2017 12:11
homa-ir.block
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Bokeh Plot</title>
<link rel="stylesheet" href="https://cdn.pydata.org/bokeh/release/bokeh-0.12.4.min.css" type="text/css" />
<script type="text/javascript" src="https://cdn.pydata.org/bokeh/release/bokeh-0.12.4.min.js"></script>
@percolator
percolator / checkiPRGResultFile.py
Created June 8, 2016 20:48
#!/usr/bin/env python
# coding: utf-8
"""
Test of file to see if it confirms to the iPRG2016 study instructios
Usage: checkiPRGResultFile.py -i input-file [-f fasta-file]
If no fasta file given, iPRG2016.fasta will be used
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percolator / my_resultFile.txt
Created June 7, 2016 22:24
"" "A1" "A2" "A3" "B1" "B2" "B3" "C1" "C2" "C3" "D1" "D2" "D3"
"HPRR4110123" 0.9499281264973647 1.0 0.9592384671711008 1.0 0.9522402757262433 1.0 1.0 1.0 1.0 0.8138319260152794 0.67724609375 1.0
"HPRR260088" 0.0 1.0 1.0 1.0 1.0 1.0 0.0021141649048625794 1.0 1.0 1.0 1.0 1.0
"HPRR3730024" 0.0 0.0 0.0 0.0 0.0 0.0 0.0021141649048625794 0.0 0.0 1.0 1.0 1.0
"HPRR3730022" 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 0.9590454692034828 1.0 1.0 1.0
"HPRR4160392" 0.9499281264973647 1.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.5327816677275621 1.0 0.4713896457765668
"HPRR4290990" 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
"HPRR4290991" 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
"HPRR4290996" 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
"HPRR4290997" 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
@percolator
percolator / iprg2016_two_peptide_rule.ipynb
Created June 7, 2016 22:16
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percolator / clust_again.ipynb
Last active May 11, 2016 07:44
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