Question

I’m having trouble with a R code that I wrote. Particularly it looks like this:

n<- nrow(aa)
for (i in 1:n)
{
A<- aa[i,]
d_ply(A, 1, function(row){  
cu<- dist(A)
    write.table(cu, file = paste(row$header, "txt", sep     = "."), sep = "\t")
}, .progress='text', .print = TRUE)
}

I would like to obtain a single file from each row of aa matrix (the file name should be the header of the row), containing the distance matrix of that row, but seems very hard. If I try the code I get this error:

cannot coerce class '"dist"' into a data.frame

How can I solve this?

Answer 1

First, assuming aa is a data frame, then A is just a single row. You don’t need to use the for loop if you’re already using d_ply, which is designed to apply something to every row of a data frame.

The second issue is that dist returns a dist object, which has to be turned into a matrix before it can be written. The following code will do that:

Third, you need to convert the row from a one-row data frame to a vector before using dist.

This leads to the following code:

d_ply(aa, 1, function(row){  
    cu<- dist(as.numeric(row[-1]))
    write.table(as.matrix(cu), file = paste(row$header, "txt", sep = "."), sep = "\t")
}, .progress='text', .print = TRUE)