Randomly subsampling seurat object-CodePudding

I've been trying to randomly subsample my seurat object. I'm interested in subsampling based on 2 columns: condition and cell type. I have 5 conditions and 5 cell types. Main goal is to have 1000 cells for each cell type in each condition. I've tried this so far:

First thing is subsetting my seurat object:

 my.list <- list(hipo.c1.neurons = hipo %>% 
                    subset(., condition %in% "c1" & group %in% "Neurons"),
                 hipo.c1.oligo = hipo %>% 
                    subset(., condition %in% "c1" & group %in% "Oligod")...etc...)

And then subsample it using sample function:

set.seed(0)
my.list.sampled <- lapply(X = my.list, FUN = function(x) {
  x <- x[,sample(ncol(x), 1000, replace = FALSE)]
})

And I get this error since there are some objects with less than 1000 cells: error in evaluating the argument 'j' in selecting a method for function '[': cannot take a sample larger than the population when 'replace = FALSE'

Then I've tried with this function:

lapply_with_error <- function(X,FUN,...){    
  lapply(X, function(x, ...) tryCatch(FUN(x, ...),
                                      error = function(e)NULL))
}

But then it gives me 0 in those objects that have less than 1000 cells. What would be the way to skip those objects that have less than 1000 cells and leave it like they are (not sample those ones)? Is there a simpler way to do this, so I don't have to subset all of my objects separately?

CodePudding user response：

I can't say for certain without seeing your data, but could you just add an if statement in the function? It looks like you're sampling column-wise, so check the number of columns. Just return x if the number of columns is less than the number you'd like to sample.

set.seed(0)
my.list.sampled <- lapply(X = my.list, FUN = function(x) {
  if(ncol(x) > 1000){
    x <- x[,sample(ncol(x), 1000, replace = FALSE)] 
  } else {
    x
  }
 })

You could make it more flexible if you want to sample something other than 1000.

set.seed(0)
my.list.sampled <- lapply(X = my.list, B = 1000, FUN = function(x, B) {
  if(ncol(x) > B){
    x <- x[,sample(ncol(x), B, replace = FALSE)] 
  } else {
    x
  }
 })