我想创建一个分类变量type
,其中样本标记为";肿瘤";如果指数的最后一个分量在01和09之间(即01-09=肿瘤(。否则,样品为";正常的";(即10-19=正常(。
clin_kipan = clin_kipan.assign(type=(
clin_kipan.index
.str.split('-')
.str[-1]
.str.contains(r'^0[1-9]', regex=True)
)).replace({'type':{True:'tumor', False:'normal'}}).dropna(axis=1)
数据(作为字典(注意:我删除了部分数据以适应stackoverflow。
meth_450_10k_kipan.iloc[:,0].to_dict((
{'TCGA-2K-A9WE-01A': 0.461440642939772,
'TCGA-2Z-A9J1-01A': 0.595894468074615,
'TCGA-2Z-A9J2-01A': 0.481304782143526,
'TCGA-2Z-A9J3-01A': 0.553849599144766,
'TCGA-2Z-A9J5-01A': 0.184349035247422,
'TCGA-2Z-A9J6-01A': 0.368324568853624,
'TCGA-2Z-A9J7-01A': 0.17338171975844,
'TCGA-2Z-A9J8-01A': 0.805217631945182,
'TCGA-2Z-A9J9-01A': 0.113336454896178,
'TCGA-2Z-A9JD-01A': 0.451013557269167,
'TCGA-2Z-A9JE-01A': 0.0734337852294042,
'TCGA-2Z-A9JG-01A': 0.452956990020555,
'TCGA-2Z-A9JI-01A': 0.606187976542221,
'TCGA-2Z-A9JJ-01A': 0.0960629248660591,
'TCGA-2Z-A9JK-01A': 0.588377732872447,
'TCGA-2Z-A9JL-01A': 0.379404812465867,
'TCGA-2Z-A9JM-01A': 0.33009261875889,
'TCGA-2Z-A9JN-01A': 0.123562375369795,
'TCGA-2Z-A9JO-01A': 0.486619960274097,
'TCGA-2Z-A9JP-01A': 0.612453055148181,
'TCGA-A4-7997-01A': 0.575299539756208,
'TCGA-A4-8098-01A': 0.872411944149227,
'TCGA-A4-8310-01A': 0.620356595911493,
'TCGA-A4-8311-01A': 0.175836950400384,
'TCGA-A4-8312-01A': 0.460360548972967,
'TCGA-AK-3425-01A': 0.553596581023431,
'TCGA-AK-3428-01A': 0.200576631432299,
'TCGA-AK-3431-01A': 0.460568866100955,
'TCGA-AK-3433-01A': 0.0667130360899875,
'TCGA-AK-3434-01A': 0.468187497808806,
'TCGA-AK-3440-01A': 0.0574998532505545,
'TCGA-AK-3445-01A': 0.736033027928183,
'TCGA-AK-3450-01A': 0.552013269922762,
'TCGA-AK-3453-01A': 0.80388456484843,
'TCGA-AK-3454-01A': 0.235022181426789,
'TCGA-AK-3458-01A': 0.414595807883066,
'TCGA-AK-3460-01A': 0.545975484391243,
'TCGA-AK-3461-01A': 0.477282040746989,
'TCGA-AL-7173-01A': 0.497670872505808,
'TCGA-AL-A5DJ-01A': 0.414268048210923,
'TCGA-AT-A5NU-01A': 0.0844509944090884,
'TCGA-B0-4688-01A': 0.126552246407372,
'TCGA-B0-4688-11A': 0.371027570539727,
'TCGA-B0-4690-01A': 0.664167690871162,
'TCGA-B0-4690-11A': 0.359369329912497,
'TCGA-B0-4691-01A': 0.726171893496605,
'TCGA-B0-4691-11A': 0.462636912871508,
'TCGA-B0-4693-01A': 0.715476004275991,
'TCGA-B0-4693-11A': 0.391904892559453,
'TCGA-B0-4694-01A': 0.541144132542648,
'TCGA-B0-4694-11A': 0.35202102740962,
'TCGA-B0-4696-01A': 0.0844268180611597,
'TCGA-B0-4696-11A': 0.450653351366657,
'TCGA-B0-4697-01A': 0.654457352712322,
'TCGA-B0-4697-11A': 0.171069365867474,
'TCGA-B0-4698-01A': 0.357248803549941,
'TCGA-B0-4698-11A': 0.48351949752012,
'TCGA-B0-4699-01A': 0.477376612682637,
'TCGA-B0-4699-11A': 0.456852387157548,
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'TCGA-B0-4703-11A': 0.370343129988362,
'TCGA-B0-4706-01A': 0.427010203528901,
'TCGA-B0-4706-11A': 0.457528590590756,
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'TCGA-B0-4710-01A': 0.746479723091997,
'TCGA-B0-4710-11A': 0.411702603771858,
'TCGA-B0-4712-01A': 0.473302353424005,
'TCGA-B0-4712-11A': 0.270372691978926,
'TCGA-B0-4713-01A': 0.560429143461328,
'TCGA-B0-4713-11A': 0.40376141612359,
'TCGA-B0-4714-01A': 0.735945131182954,
'TCGA-B0-4714-11A': 0.263599330925764,
'TCGA-B0-4718-01A': 0.833718331254908,
'TCGA-B0-4718-11A': 0.379442535687981,
'TCGA-B0-4810-01A': 0.699637311093991,
'TCGA-B0-4810-11A': 0.479396092302295,
'TCGA-B0-4811-01A': 0.531909129769779,
'TCGA-B0-4811-11A': 0.54226596375653,
'TCGA-B4-5835-01A': 0.717016504186623,
'TCGA-B4-5836-01A': 0.693534883907721,
'TCGA-B4-5838-01A': 0.508256362230539,
'TCGA-B4-5843-01A': 0.487548027975282,
'TCGA-B4-5844-01A': 0.649681573187955,
'TCGA-B8-4146-01B': 0.82401932868328,
'TCGA-B8-4153-01B': 0.460999849292442,
'TCGA-B8-4621-01A': 0.381802967801001,
'TCGA-B8-4622-01A': 0.670973304749735,
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'TCGA-B8-5162-01A': 0.351204810616952,
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'TCGA-B8-5551-01A': 0.510539456362485,
'TCGA-B8-5552-01B': 0.561914284053566,
'TCGA-B8-5553-01A': 0.721040148269779,
'TCGA-B8-A54D-01A': 0.569601921914092,
'TCGA-B8-A54E-01A': 0.287289206223702,
'TCGA-B8-A54F-01A': 0.757363680231869,
'TCGA-B8-A54G-01A': 0.835557016199056,
'TCGA-B8-A54H-01A': 0.495744985734965,
'TCGA-B8-A54I-01A': 0.395012393085408,
'TCGA-B8-A54J-01A': 0.406091467819355,
'TCGA-B8-A54K-01A': 0.833006431093696,
'TCGA-B8-A7U6-01A': 0.61310478518293,
'TCGA-B8-A8YJ-01A': 0.364804929088756,
'TCGA-B9-5155-01A': 0.360402370593871,
'TCGA-B9-5156-01A': 0.48035755488036,
'TCGA-B9-7268-01A': 0.188844826257322,
'TCGA-B9-A44B-01A': 0.362254621945938,
'TCGA-B9-A5W7-01A': 0.703654140729989,
'TCGA-B9-A5W8-01A': 0.270043280449106,
'TCGA-B9-A5W9-01A': 0.824048307585993,
'TCGA-B9-A69E-01A': 0.61780736246742,
'TCGA-B9-A8YH-01A': 0.226240912502849,
'TCGA-B9-A8YI-01A': 0.690382207755967,
'TCGA-BP-4177-01A': 0.725375025466823,
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'TCGA-Y8-A896-01A': 0.276383911326578,
'TCGA-Y8-A897-01A': 0.374250450339407,
'TCGA-Y8-A898-01A': 0.310842285574522,
'TCGA-Y8-A8RY-01A': 0.552137271695761,
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'TCGA-Y8-A8S0-01A': 0.264547845506278,
'TCGA-Y8-A8S1-01A': 0.581694254362101}
预期结果:
行的总数为867,其中662个预期为tumor
,其余为normal
。
len(meth_450_10k_kipan)
867
meth_450_10k_kipan.index.str.split('-').str[-1].str.contains(r'^0[1-9]', regex=True).sum()
662
您可以分两步完成,提取标签,然后根据其值进行过滤,以分配所需的输出:
df = pd.Series(d).to_frame() # assuming d to be the dict with the data
labels = df.index.str.extract(r"-(d+)D+$")[0].astype(int)
df["labels"] = pd.Categorical((labels < 10).map({True: "tumor", False: "normal"}))
>> df["labels"].unique()
['tumor', 'normal']
Categories (2, object): ['normal', 'tumor']
>> df["labels"]
TCGA-2K-A9WE-01A tumor
TCGA-2Z-A9J1-01A tumor
TCGA-2Z-A9J2-01A tumor
TCGA-2Z-A9J3-01A tumor
TCGA-2Z-A9J5-01A tumor
...
TCGA-Y8-A898-01A tumor
TCGA-Y8-A8RY-01A tumor
TCGA-Y8-A8RZ-01A tumor
TCGA-Y8-A8S0-01A tumor
TCGA-Y8-A8S1-01A tumor
Name: labels, Length: 637, dtype: category
Categories (2, object): ['normal', 'tumor']