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Intersection 5 sets of genes and retrieval of specific subsets

Hey all,

i need to intersect 5 sets of genes and retrieve all possible subsets, meaning the ones common to just 1, the ones in common in any 2/5, the ones common in any 3/5, any 4/5 and 5/5. So in the end my output ideally would be 5 "private" sets + 4 other sets (2/5,3/5,4/5,5/5).
important: i want to retrieve them, not visualize them.

Anyone has a quick way to do it?

r genes intersections
• 1,817 views • link
updated by noorpratap.singh noorpratap.singh • written by lessismore lessismore

1 answer 

get.int.genes <- function(genes.list)
{
  total.genes <- Reduce(union, genes.list)
  genes.req <- list()
  for(i in c(paste('only ', c(1:5)), paste("common ", c(2:5))))
    genes.req[[i]] <- c()
  for(gene in total.genes)
  {
    count = 0
    set.ind = 0
    for(j in seq_along(genes.list))
    {
      if(gene %in%  genes.list[[j]])
      {
        count = count + 1
        set.ind = j
      }
    }
    if(count == 1)
      genes.req[[paste('only ', set.ind)]] <- c(genes.req[[paste('only ', set.ind)]], gene)
    else
      genes.req[[paste('common ', count)]] <- c(genes.req[[paste('common ', count)]], gene)
  }
  return(genes.req)
}

This function should help with only denoting the 5 different sets and common denoting what you require.

• 0 views • link
written by noorpratap.singh noorpratap.singh

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