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New data sets

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This commit is contained in:
Neil Lawrence 2014-05-24 15:31:42 +01:00
parent c291d5b2ad
commit de75d7dac1
2 changed files with 65 additions and 1 deletions
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36
GPy/util/datasets.py
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@ -375,7 +375,43 @@ def sod1_mouse(data_set='sod1_mouse'):
num_cond=4
X = 1
return data_details_return({'X': X, 'Y': Y}, data_set)
def spellman_yeast(data_set='spellman_yeast'):
if not data_available(data_set):
download_data(data_set)
from pandas import read_csv
dirpath = os.path.join(data_path, data_set)
filename = os.path.join(dirpath, 'combined.txt')
Y = read_csv(filename, header=0, index_col=0, sep='\t')
return data_details_return({'Y': Y}, data_set)
def spellman_yeast_cdc(data_set='spellman_yeast'):
if not data_available(data_set):
download_data(data_set)
from pandas import read_csv
dirpath = os.path.join(data_path, data_set)
filename = os.path.join(dirpath, 'combined.txt')
Y = read_csv(filename, header=0, index_col=0, sep='\t')
t = np.asarray([10, 30, 50, 70, 80, 90, 100, 110, 120, 130, 140, 150, 170, 180, 190, 200, 210, 220, 230, 240, 250, 270, 290])
times = ['cdc15_'+str(time) for time in t]
Y = Y[times].T
t = t[:, None]
return data_details_return({'Y' : Y, 't': t, 'info': 'Time series of synchronized yeast cells from the CDC-15 experiment of Spellman et al (1998).'}, data_set)
def lee_yeast_ChIP(data_set='lee_yeast_ChIP'):
if not data_available(data_set):
download_data(data_set)
from pandas import read_csv
import zipfile
dirpath = os.path.join(data_path, data_set)
filename = os.path.join(dirpath, 'binding_by_gene.tsv')
X = read_csv(filename, header=1, index_col=0, sep='\t')
transcription_factors = [col for col in X.columns if col[:7] != 'Unnamed']
annotations = X[['Unnamed: 1', 'Unnamed: 2', 'Unnamed: 3']]
X = X[transcription_factors]
return data_details_return({'annotations' : annotations, 'X' : X, 'transcription_factors', transcription_factors}, data_set)
def fruitfly_tomancak(data_set='fruitfly_tomancak', gene_number=None):
if not data_available(data_set):
download_data(data_set)