Databases
StackOverflow2013
Postsdbo
POR - function simplification and optimization
 

Note that there are some explanatory texts on larger screens.

plurals
  1. POR - function simplification and optimization
    primarykey
    data
    text
    <p>What the function does is finds the <code>primes</code> in <code>list1</code> and converts them to their equivalent <code>a</code> (i.e. 2 would be <code>a2</code> which is 1,1). Then it takes the <code>!NULL</code> in <code>list2</code> and searches if it is present in the converted <code>list1</code> (converted to a list of two of 1,2,3, or 4). Finally it returns a logical list of true and false which will be used later on. Even tough it works it looks really inefficient and long. Looking for any suggestions to improve this. </p> <p>Test data:</p> <pre><code>list1&lt;-c(11,2,29,5,17) offspring&lt;-data.frame(matrix(unlist(list1), nrow=1, byrow=T)) list2&lt;-c(0,11) parent&lt;-data.frame(matrix(unlist(list2), nrow=1, byrow=T)) </code></pre> <p>Prerequisites:</p> <pre><code>primes &lt;- c(2, 3, 5, 7, 11, 13, 17, 19, 23, 29) a2 &lt;- c(1,1) a3 &lt;- c(1,2) a5 &lt;- c(2,2) a7 &lt;- c(1,3) a11 &lt;- c(1,4) a13 &lt;- c(2,3) a17 &lt;- c(2,4) a19 &lt;- c(3,3) a23 &lt;- c(3,4) a29 &lt;- c(4,4) </code></pre> <p>The missing function:</p> <pre><code>missing &lt;- function(offspring, parent){ ofls &lt;- lapply(1:ncol(offspring),FUN = function(i){get(paste0("a", offspring[i]))}) pals &lt;- lapply(1:length(parent[parent&gt;0]),FUN = function(i){get(paste0("a", parent[parent&gt;0]))}) ofls&lt;-data.frame(ofls) pals&lt;-data.frame(pals) set1&lt;- matrix(,nrow=10,ncol=1) set2&lt;- matrix(,nrow=10,ncol=1) for(z in 1:5){ set1[z,]&lt;-match(ofls[1,z],pals[1,], nomatch=0) set1[z+5,]&lt;-match(ofls[2,z],pals[1,], nomatch=0) set2[z,]&lt;-match(ofls[1,z],pals[2,], nomatch=0) set2[z+5,]&lt;-match(ofls[2,z],pals[2,], nomatch=0) } return((set1+set2)[c(1,2,3,4,5)]+(set1+set2)[c(6,7,8,9,10)]==0) } missing(offspring,parent) </code></pre> <p>Result:</p> <pre><code>[1] TRUE TRUE FALSE TRUE FALSE </code></pre> <p>EDIT: I corrected the mistake I found, in doing so the script go simplified a lot.</p> <p>EDIT 2: I am still getting an error in RStudio after running the function and then trying to <code>view()</code> the two data.frames:</p> <pre><code>Error in View : argument "title" is missing, with no default </code></pre>
    singulars
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. PTQuestion
    1. UScrysis405
    1. UScrysis405
    plurals
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. COI have tried understanding the code but its not making any sense. Can you explain what is the point of those ax variables and what is the goal of the "missing" function
      singulars
      1. POR - function simplification and optimization
      1. USRohit Das
    2. COThese are alleles. 0 is a missing allele.`parents(0 AA) offspring(TT CT AA CC AT)`. The point of the function is to find mendelian errors even though one of the parents alleles is missing. So, in the above case an A has to be in all offsprings. I tried to do this by splitting up the alleles into 1,2,3,4 hence the ax variables.
      singulars
      1. POR - function simplification and optimization
      1. UScrysis405
    3. COI think I have a mistake somewhere in there (trying to find it now)
      singulars
      1. POR - function simplification and optimization
      1. UScrysis405
 

Querying!

 
Guidance
A row detail

Detail views are divided into sections. All the information in the data section comes from columns in the selected row. The other sections display data from other, related rows.

Related data can be related in a to-one or a to-many fashion. Captions of data related in a to-many fashion link to a list view showing a filtered view of the table.

Try moving around until you find a non-empty to-many entry and click on the label to get to one. You can move back to the root by clicking on the database name in the header.

SQuiL has stopped working due to an internal error.

If you are curious you may find further information in the browser console, which is accessible through the devtools (F12).

Reload