how i can set a function that works for all column of a data frame or matrix in R?

Question

I have a data frame with 1000 rows and 10000 columns, I want to set a function of estimating v(corresponds to 2pq) for each column. sample data can be

data=data.frame(replicate(1000,sample(0:2,100,rep=T))) #[1000 snp (column) and 100 ind (row)]

I can calculate v for the first row

a=count(data$X1==2) #totla no of 2
b=count(data$X1==1) #total no of 1
n=nrow(data)        #no of row in real data NA can be there
p=(a+(b*0.5))/n
q=1-p
v=2*p*q
v

I want to estimate v for all the columns. Thanks in advance

Answer 1

Put the code in a function.

calculate <- function(v) {
  a=sum(v==2) 
  b=sum(v==1) 
  n=length(v) 
  p=(a+(b*0.5))/n
  q=1-p
  v=2*p*q
  v
}

and if you have a dataframe use sapply to calculate v for all columns.

result <- sapply(data, calculate)

You can also use apply with MARGIN = 2 which will work for both dataframe and matrix.

result <- apply(data, 2, calculate)

Answer 2

We can use dapply

library(collapse)
dapply(data, calculate)

where

calculate <- function(v) {
  a=sum(v==2) 
  b=sum(v==1) 
  n=length(v) 
  p=(a+(b*0.5))/n
  q=1-p
  v=2*p*q
  v
}