Getting Started with Analysis in Python: NumPy, Pandas and ...
嚜澶etting Started with
Analysis in Python:
NumPy, Pandas and Plotting
Bioinformatics and Research Computing (BaRC)
NumPy
? Numerical Python
? Efficient multidimensional array processing
and operations
每 Linear algebra (matrix operations)
每 Mathematical functions
? Array (objects) must be of the same type
>>>import numpy as np
>>>np.array([1,2,3,4],float)
2
NumPy: Slicing
McKinney, W., Python for Data Analysis, 2nd Ed. (2017)
3
Pandas
? Efficient for processing tabular, or panel, data
? Built on top of NumPy
? Data structures: Series and DataFrame (DF)
每 Series: one-dimensional , same data type
每 DataFrame: two-dimensional, columns of different data types
每 index can be integer (0,1,#) or non-integer ('GeneA','GeneB',#)
index
Gene
Series
Expression
GeneA
3.51
GeneB
0.44
GeneC
5.21
GeneD
4.55
GeneE
6.78
index
DataFrame
GTEX1117F
Gene
GTEX111CU
GTEX111FC
0
DDX11L1
0.1082
1
WASH7P
21.4
2
MIR1302-11
3
FAM138A
4
OR4G4P
0
0
0
5
OR4F5
0
0
0
axis = 1
0.1158 0.02104
11.03
16.75
axis = 0
0.1602 0.06433 0.04674
0.05045
0 0.02945
4
What can you do with a
Pandas DataFrame?
? Filter
每 Select rows/columns
? Sort
? Numerical or Mathematical operations (e.g.
mean)
? Group by column(s)
? Many others!
5
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