CODEWITHSUNDEEP
rloopsmatrix-multiplication
bioinformatics2020
bioinformatics2020

Reputation: 89

Correlation Matrix Between Two Dataframes in R

I have two s:

dataframe1

name1 500
name2 394
name3 344
...
name2000 300

dataframe2

name1 200
name2 194
name3 44
...
name2000 100

And an empty 2000X2000 matrix (empty.matrix)

What I want is to fill this matrix with correlation values between the two s. So that the first element in df1 will have a correlation value with every element of df2... up until element 2000. I am doing this through the following code:

for (i in 1:2000) {
  for (j in 1:2000){ 
    empty.matrix[i,j] <- cor(df1$V1[[i]],df2$V2[[j]])
    }
}

Problem is, this is taking forever. Anybody have a quicker way of getting this through? Thanks!

Upvotes: 2

Views: 2283

Answers (1)

B. Christian Kamgang
B. Christian Kamgang

Reputation: 6489

assuming that your data frames have the same number of rows, the following code should work: 

cor(dataframe1, dataframe2)

Here is an example using the mtcars data set in R:

cor(mtcars[1:5], mtcars[6:11])
         wt        qsec         vs         am       gear       carb
mpg  -0.8676594  0.41868403  0.6640389  0.5998324  0.4802848 -0.5509251
cyl   0.7824958 -0.59124207 -0.8108118 -0.5226070 -0.4926866  0.5269883
disp  0.8879799 -0.43369788 -0.7104159 -0.5912270 -0.5555692  0.3949769
hp    0.6587479 -0.70822339 -0.7230967 -0.2432043 -0.1257043  0.7498125
drat -0.7124406  0.09120476  0.4402785  0.7127111  0.6996101 -0.090789

Upvotes: 4

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