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  • elizabeth000
    replied
    Actually the solution was super easy! You have to use double [[ to index a list! This works:

    Code:
    extest = list()
    k = 1
    for(i in 1:nlevels(data$samples$group)) {
       for(j in (i+1):nlevels(data$samples$group)) {
          if (i < nlevels(data$samples$group)) {
             extest[[k]] = exactTest(data, pair=c(i,j))
             k = k+1
          }
       }
    }

    Leave a comment:


  • elizabeth000
    replied
    For the moment this works, but is really not ideal.
    Code:
    for(i in 1:nlevels(data$samples$group)) {
       for(j in (i+1):nlevels(data$samples$group)) {
          if (i < nlevels(data$samples$group)) {
             et = exactTest(data, pair=c(i,j))
             filen = paste("/media/liz/ACERDATA/Elizabeth_DATA/exacttest_dev_cds", i, j, ".txt", sep="")
             #Open output file
             sink(filen)
             print(et$comparison)
             print(topTags(et, n=100))
             #Close output file
             sink()
          }
       }
    }

    Leave a comment:


  • elizabeth000
    replied
    Yes, that's what I was thinking. Instead of filling indices with list objects, I should append the new result to the list. Hmmmm but how do I do that in R?
    I'm drawing a blank...

    Leave a comment:


  • dpryan
    replied
    Try making the empty list first and then adding to it, since that will match all the coercion processes going on in in your real code.

    Leave a comment:


  • elizabeth000
    replied
    > first = exactTest(data,pair=c(1,2))
    > second = exactTest(data,pair=c(2,3))
    > results = list(first,second)
    > results
    [[1]]
    An object of class "DGEExact"
    $table
    logFC logCPM PValue
    CGI_10000009 -2.3851234 1.493044 0.1171040419
    CGI_10000013 0.1844446 4.147738 0.7403461115
    CGI_10000014 -4.9376158 2.707417 0.0001137864
    CGI_10000015 0.4967844 3.773692 0.4339343285
    CGI_10000028 -0.2890212 2.476181 0.9883519753
    18055 more rows ...

    $comparison
    [1] "28cell" "blastula"

    $genes
    NULL


    [[2]]
    An object of class "DGEExact"
    $table
    logFC logCPM PValue
    CGI_10000009 -2.57188463 1.493044 0.8000000
    CGI_10000013 0.01444976 4.147738 1.0000000
    CGI_10000014 0.41462168 2.707417 0.9686494
    CGI_10000015 -0.36575812 3.773692 0.6137249
    CGI_10000028 0.64099475 2.476181 0.7954756
    18055 more rows ...

    $comparison
    [1] "blastula" "dlarvae"

    $genes
    NULL

    That seems to work... so why doesn't it work in my loop...

    Leave a comment:


  • dpryan
    replied
    Not sure then, I'd have to play around with it. You might just play around with making a list of two instance by hand.

    Leave a comment:


  • elizabeth000
    replied
    By declaring extest as a list:

    Code:
    extest = list()
    k = 1
    for(i in 1:nlevels(data$samples$group)) {
       #print(c(i,"i"))
       for(j in (i+1):nlevels(data$samples$group)) {
          if (i < nlevels(data$samples$group)) {
             extest[k] = exactTest(data, pair=c(i,j))
             #print(et$table)
             k = k+1
          }
       }
    }
    I get this warning for each execution of exactTest:
    28: In extest[k] = exactTest(data, pair = c(i, j)) :
    number of items to replace is not a multiple of replacement length

    > class(extest)
    [1] "list"
    > class(extest[1])
    [1] "list"

    Leave a comment:


  • dpryan
    replied
    You might have to change extest to a list itself, since I'm not sure how/if coercion works in this scenario.

    Leave a comment:


  • elizabeth000
    replied
    I find that extest[1] is a list:

    > class(extest[1])
    [1] "list"

    whereas it should be:

    > class(extest)
    [1] "DGEExact"
    attr(,"package")
    [1] "edgeR"

    So I need to find out how to store the DGEExact objects somewhere while creating them in the loop. There must be a way to do this????

    Leave a comment:


  • elizabeth000
    replied
    Thank you for your fast reply. Yes, this was completely wrong, and I fixed a few problems. Here is the complete loop:

    Code:
    extest = c()
    k = 1
    for(i in 1:nlevels(data$samples$group)) {
       print(c(i,"i"))
       for(j in (i+1):nlevels(data$samples$group)) {
          if (i < nlevels(data$samples$group)) {
             extest[k] = exactTest(data, pair=c(i,j))
             k = k+1
          }
       }
    }
    This is improved because it tests each pair only once, and I prevented extest from being overwritten. But... extest[k] is not structured as expected... for example, I cannot view head(extest[1]), the whole list prints to screen. And:

    > extest[1]$comparison
    NULL

    How can this strange behavior be explained? Is there any way to store DGEExact objects in a list or other R class?

    Leave a comment:


  • dpryan
    replied
    You need to create "extext" beforehand, that's why it's complaining that it can't be found. Just add this above your while loop:
    Code:
    extest = c()
    Of course, you'll have to deal with extest after the while loop or it'll get over-written.

    Leave a comment:


  • elizabeth000
    started a topic Working with DGEExact objects in a loop

    Working with DGEExact objects in a loop

    Objects of class DGEExact are the result of the exactTest() function in edgeR. I'm having trouble making loops to assign DGEExact objects to a variable. I'm probably making some very basic mistake in handling R data types...?

    > nlevels(data$samples$group)
    [1] 8

    Code:
    for(i in 1:nlevels(data$samples$group)) {
       index = 1
       while(index < nlevels(data$samples$group)) {
          extest[i] = exactTest(data, pair=c(i,1+index),)
          index = index + 1
       }
    }
    Error in extest[i] = exactTest(data, pair = c(i, 1 + index), ) :
    object 'extest' not found

    Sorry for the basic question, I hope it is easy to answer!

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