Cancer Mutation Data Analysis

Question

[kulani.s91]

I have a data set consisting of mutation data and NaN and NA values as shown below.

GENE    X115    X1154   X1156
AAMP    NaN         NaN         NaN
AARS2   NaN        NaN          NaN
ABCA9   Q10*    NaN         NaN
ABCB1   NA          NA           NA

Is there a way to maintain the NA and NaN values and analyse the data set using apcluster in R-Programming?

[Ram]

Most commands in R have an option along the lines of na.rm. No such option here?

[kulani.s91]

Thank you for the reply. The na.rm() handles the NA values, but I need a method to handle the NaN values since apcluster does not output the correct answer or runs across an error when the NaN values are present.

[Kritika]

U can replace NaN to NA or with 0 and then you can re run code

[Ram]

Either this or R also has an option (na.values) I think, to denote what values should be considered NA

[Ram]

Also, please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 1

[Kritika]

u can use this

 apcluster(na.omit(your_data_set))