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I am trying to make a paired matrix of gene-gene correlation. Considering that I have a huge matrix (13000 genes and 900 samples) and for some reasons I don't want to decrease the number of my genes, my gene-correlation matrix would be 13000*13000 and my paired matrix will become 169 million *4 (Column 1: Gene 1; Column 2 : Gene 2; Column 3: Correlations; Column 4: P-values) . In this case, I have to exclude unnecessary calculations as much as I can. I have excluded the situation that Gene 1 = Gene 2. But I couldn't find a way to exclude the condition that "Column 1: Gene 1 ; Column 2: Gene 2 = Column 1: Gene 2; Column 2: Gene 1 ". To make a long story short, correlation between G1 and G2 is equal to G2 and G1. It is like calculating just lower section of diag in a symmetric matrix. I would be grateful if anybody help me in this case. I have enclosed my python codes here:

import pandas as pd
import numpy as np
import scipy
import math
import openpyxl
from openpyxl import Workbook
from scipy.stats import spearmanr


din=pd.read_csv('m_test.csv', index_col=0)

out=pd.DataFrame()
outdf=pd.DataFrame()

for g1 in din.index:
    for g2 in din.index:
        temp=din.loc[[g1, g2]]
        if g1==g2:
            next
        else: 
            spR, spP=spearmanr(temp.loc[g1], temp.loc[g2])
            frame={'g1':[g1], 'g2':[g2], 'spR':[spR], 'spP':[spP]}

            out=pd.DataFrame(frame)

            outdf=pd.concat([outdf, out])
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You don't need g2 to go from 0 to din.index, just from 0 to g1 - 1. This way, you'll end up calculating just for the "lower triangle":

g1-> 0   1   2   3
g2
0                    #(0,0 to 0,1-1 = nothing)
1    X               #(1,0 to 1,1-1 = 1,0)
2    X   X           #(2,0 to 2,2-1 = 2,0; 2,1)
3    X   X   X       #(3,0 to 3,3-1 = 3,0; 3,1 and 3,2)
4    X   X   X   X   #(4,0 to 4,4-1 = 4,0; 4,1; 4,2 and 4,3)
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  • $\begingroup$ Thank you very much. It works this way. $\endgroup$ – Elyas Mohammadi Feb 13 at 9:45
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Actually I found an easy and efficient way.

import pandas as pd
import numpy as np
import scipy
import math
import openpyxl
from openpyxl import Workbook
from scipy.stats import pearsonr
from scipy.stats import spearmanr
from scipy.stats import kendalltau

pro=pd.read_csv('m_test.csv', index_col=0)

xInds = []
yInds = []
for i in range(len(pro.index)):
    for j in range(i+1, len(pro.index)):
        xInds.append(i)
        yInds.append(j)

z=0
Rlist_sp = []
Plist_sp = []
Rlist_pe = []
Plist_pe = []
while z < len(xInds):
    b=xInds[z]
    c=yInds[z]

    spR, spP = spearmanr(pro.iloc[b].values, pro.iloc[c].values)
    peR, peP = pearsonr(pro.iloc[b].values, pro.iloc[c].values) 

    Rlist_sp.append(spR)
    Plist_sp.append(spP)
    Rlist_pe.append(peR)
    Plist_pe.append(peP)    
    z=z+1 

G1=pd.DataFrame(xInds)
G2=pd.DataFrame(yInds)
R_sp=pd.DataFrame(Rlist_sp)
P_sp=pd.DataFrame(Plist_sp)
R_pe=pd.DataFrame(Rlist_pe)
P_pe=pd.DataFrame(Plist_pe)        

Final=pd.concat([G1, G2, R_sp, P_sp, R_pe, P_pe], axis=1)
np.savetxt('Final_gg_A549.txt', Final.values, fmt='%s', delimiter='\t')  
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