CODEWITHSUNDEEP
r
jessy
jessy

Reputation: 311

Applying threshold on correlation matrix in R

I am currently working on a dataset using R. I have created a correlation martix(Pearson) for my variables.But now I want to put a threshold for the values shown in matrix. I am trying the following code:

cor_relation = cor(mydata_frame, use="all.obs", method="pearson")

I get the following output:

             200605_s_at      202592_at      202958_at
200605_s_at  1.000000000     0.295065389     0.169772244
202592_at    0.695065389     1.000000000     -0.534394180
202958_at    0.869772244     -0.534394180    1.000000000

I want to find the following output(when i put the threshold 0.6):

             200605_s_at      202592_at      202958_at
200605_s_at  1.000000000        NA              NA
202592_at    0.695065389     1.000000000        NA
202958_at    0.869772244        NA           1.000000000

Thanks in advance for help!

Upvotes: 4

Views: 6676

Answers (2)

BrodieG
BrodieG

Reputation: 52637

An alternate:

cor_relation[abs(cor_relation) < 0.6] <- NA

Upvotes: 7

Sven Hohenstein
Sven Hohenstein

Reputation: 81693

is.na(cor_relation) <- abs(cor_relation) < 0.6

will replace all coefficients with an absolute value of less than 0.6 with NA.

Upvotes: 5

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