Python GTestYates Examples

Example #1

File: pValuePlot.py Project: IUEayhu/STAMP

import random

from stamp.metagenomics.plugins.statisticalTests.Fishers import Fishers
from stamp.metagenomics.plugins.statisticalTests.ChiSquare import ChiSquare
from stamp.metagenomics.plugins.statisticalTests.ChiSquareYates import ChiSquareYates
from stamp.metagenomics.plugins.statisticalTests.GTest import GTest
from stamp.metagenomics.plugins.statisticalTests.GTestYates import GTestYates
from stamp.metagenomics.plugins.statisticalTests.Permutation import Permutation
from stamp.metagenomics.plugins.statisticalTests.DiffBetweenProp import DiffBetweenProp
from stamp.metagenomics.plugins.statisticalTests.Bootstrap import Bootstrap

fishers = Fishers()
chiSquare = ChiSquare()
chiSquareYates = ChiSquareYates()
gTest = GTest()
gTestYates = GTestYates()
permutation = Permutation()
diffBetweenProp = DiffBetweenProp()
bootstrap = Bootstrap()

sampleSize = 50


def mean(x):
    if len(x) == 0:
        return 0

    sum = 0.0
    for i in xrange(0, len(x)):
        sum += x[i]
    return sum / len(x)

Example #2

from stamp.metagenomics.plugins.statisticalTests.Fishers import Fishers
from stamp.metagenomics.plugins.statisticalTests.ChiSquare import ChiSquare
from stamp.metagenomics.plugins.statisticalTests.ChiSquareYates import ChiSquareYates
from stamp.metagenomics.plugins.statisticalTests.GTest import GTest
from stamp.metagenomics.plugins.statisticalTests.GTestYates import GTestYates
from stamp.metagenomics.plugins.statisticalTests.Permutation import Permutation
from stamp.metagenomics.plugins.statisticalTests.DiffBetweenProp import DiffBetweenProp
from stamp.metagenomics.plugins.statisticalTests.Bootstrap import Bootstrap
from stamp.metagenomics.plugins.statisticalTests.Barnard import Barnard

fishers = Fishers()
chiSquare = ChiSquare()
chiSquareYates = ChiSquareYates()
gTest = GTest()
gTestYates = GTestYates()
permutation = Permutation()
diffBetweenProp = DiffBetweenProp()
bootstrap = Bootstrap()
barnard = Barnard()

sampleSizes = [5, 10, 15, 25]


def mean(x):
    if len(x) == 0:
        return 0

    sum = 0.0
    for i in xrange(0, len(x)):
        sum += x[i]

Example #3

File: alphaTest.py Project: IUEayhu/STAMP

import random

from stamp.metagenomics.plugins.statisticalTests.Fishers import Fishers
from stamp.metagenomics.plugins.statisticalTests.GTest import GTest
from stamp.metagenomics.plugins.statisticalTests.GTestYates import GTestYates
from stamp.metagenomics.plugins.statisticalTests.DiffBetweenProp import DiffBetweenProp

fishers = Fishers()
gTest = GTest()
gTestYates = GTestYates()
diffBetweenProp = DiffBetweenProp()

numReplicates = 10000             # number of samples to draw

popSize = 1000000       # size of underlying population
propInSS = [0.1]       # proportion of sequences in subsystem (SS) of interest

sampleSize1 = [1000]    # sample size for community 1
sampleSize2 = [2000]    # sample size for community 2

for sampleSizeIndex in xrange(0, len(sampleSize1)):
  print 'Considering communities with a sample size of: ' + str(sampleSize1[sampleSizeIndex]) + ' and ' + str(sampleSize2[sampleSizeIndex])
  for prop in propInSS:
    print '  Proportion of sequences in subsystem of interest: ' + str(prop)
          
    totalSamples1 = sampleSize1[sampleSizeIndex]
    totalSamples2 = sampleSize2[sampleSizeIndex]
    
    fishersResults = []
    gTestResults = []
    gTestYatesResults = []