python - 在表达式数据集python中删除值

问题描述

我有这个微阵列数据集。我想绕过我在这个管道的早期版本中遇到的一个问题，（https://geoparse.readthedocs.io/en/latest/Analyse_hsa-miR-124a-3p_transfection_time-course.html）我创建了一个实验文件并将其作为数据框读入。我想消除我的表达式表中不再作为字符串值存在于我读入的数据框的列访问中的每一列。

# Import tools
import GEOparse
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt

# download datasets
gse1 = GEOparse.get_GEO(geo="GSE99039", destdir="C:/Users/Highf_000/PycharmProjects/TFTest")
gse2 = GEOparse.get_GEO(geo="GSE6613", destdir="C:/Users/Highf_000/PycharmProjects/TFTest")
gse3 = GEOparse.get_GEO(geo="GSE72267", destdir="C:/Users/Highf_000/PycharmProjects/TFTest")

# import all GSM data for each GSE file
with open("GSE99039_GPL570.csv") as f:
    GSE99039_GPL570 = f.read().splitlines()
with open("GSE6613_GPL96.csv") as f:
    GSE6613_GPL96 = f.read().splitlines()
with open("GSE72267_GPL571.csv") as f:
    GSE72267_GPL571 = f.read().splitlines()

# gse1
gse1.gsm = gse1.phenotype_data
print(gse1.gsm.head())

# gse1
gse1.details = pd.read_csv('GSE99039_MicroarrayDetails.csv', delimiter = ',')
print(gse1.details.head())
gse1.detailsv1 = gse1.details[(gse1.details.values == "CONTROL") | (gse1.details.values == "IPD") | (gse1.details.values == "GPD") ]
print(gse1.detailsv1.head())

# gse1
pivoted_control_samples = gse1.pivot_samples('VALUE')[GSE99039_GPL570]
print(pivoted_control_samples)


# gse1
# Pulls the probes out
pivoted_control_samples_average = pivoted_control_samples.median(axis=1)
# Print number of probes before filtering
print("Number of probes before filtering: ", len(pivoted_control_samples_average))
# Extract all probes > 0.25
expression_threshold = pivoted_control_samples_average.quantile(0.25)
expressed_probes = pivoted_control_samples_average[pivoted_control_samples_average >= expression_threshold].index.tolist()
# Print probes above cut off
print("Number of probes above threshold: ", len(expressed_probes))
# confirm filtering worked
samples = gse1.pivot_samples("VALUE").loc[expressed_probes]
print(samples.head())

# print phenotype data
print(gse1.phenotype_data[["title", "source_name_ch1", "Disease_Label", "Sex" ]])

这就是我创建的数据框的样子，gse1.detailsv1在脚本中命名：

   Accession       Title  Source name  ... Subject_id Disease label     Sex
0  GSM2630758  E7R_039a01  Whole blood  ...      L3012       CONTROL  Female
1  GSM2630759  E7R_039a02  Whole blood  ...      L2838           IPD    Male
2  GSM2630760  E7R_039a03  Whole blood  ...      L2540           IPD  Female
3  GSM2630761  E7R_039a04  Whole blood  ...      L3015       CONTROL  Female
4  GSM2630762  E7R_039a05  Whole blood  ...      L2884           IPD  Female

[5 rows x 7 columns]

这是我的表达式表的样子，samples在脚本中命名：

name       GSM2630758  GSM2630759  ...  GSM2631314  GSM2631315
ID_REF                             ...                        
1007_s_at       5.397       4.952  ...       5.567       5.529
1053_at         5.199       5.198  ...       5.706       5.078
117_at          8.327       8.589  ...       8.511       8.458
121_at          7.042       6.935  ...       7.526       7.673
1294_at         7.753       8.210  ...       7.537       7.418

[5 rows x 558 columns]

假装，如果第一个数据帧的加入列中不存在 GSM2630758，我想删除 GSM2630758。我需要循环并消除所有不再存在的值。

标签： pythonloopsmergegenetics

python - 在表达式数据集python中删除值

问题描述

解决方案

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