Is there a way to get `cor` to work?

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#90 opened on Apr 15, 2021 0 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 4/5
Estimated time: 3-5 days
Newbie friendliness: 42/100

Issue type: Feature
Clarity: Mostly clear
Activity status: Stale
Tech stack: r
Domain: data

Research direction

Start by reproducing the reported cor(DelayedArray(x), DelayedArray(y)) error and compare it with the supplied delayedCov examples. Use the Pearson correlation behavior described in the issue as the target, and verify that equivalent matrix and DelayedArray inputs produce matching results without the numeric-type error.

Written by the indexing model from the issue text.

Description

When I try cor, I get errors like Error in cor(DelayedArray(x), DelayedArray(y)) : 'x' must be numeric. Am I missing something simple?

If it's not implemented, I have a little function for this and I could send a pull request.

#' Drop-in replacement for cov or cor; tolerates DelayedArray input. Pearson correlation only. 
#'
delayedCov = function(x, y = x, do_cor = F){
  mux = colMeans(x)
  muy = colMeans(y)
  zx = sweep(x, 2, mux, "-")
  zy = sweep(y, 2, muy, "-")
  covxy = t(zx) %*% zy
  covxy = covxy / nrow(x)
  if(do_cor){
    sx = sqrt(colMeans(zx^2))
    sy = sqrt(colMeans(zy^2))
    covxy = Matrix::Diagonal(x = 1/sx) %*% covxy %*% Matrix::Diagonal(x = 1/sy)
  }
  covxy
}
# tests
x = matrix(rnorm(1000), ncol = 10)
y = matrix(rnorm(1000), ncol = 10)
plot(delayedCov(x, y),  cov(x, y)); abline(a = 0, b = 1)
plot(delayedCov(x, y, do_cor = T),  cor(x, y)); abline(a = 0, b = 1)
plot(delayedCov(DelayedArray(x), DelayedArray(y), do_cor = T),  cor(x, y)); abline(a = 0, b = 1)

Dominant language: R
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