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POImplementing simple scoring function with permutation test in R
 

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  1. POImplementing simple scoring function with permutation test in R
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    <p>I'm new in R, and I want to calculate some specific score for bunch of genes in biology. can somebody help me to implement this ? :-)</p> <p>I have following two vectors: </p> <pre><code>vector 1: (0.01,0.02,0.04,0.5,0.9,0.002,0.07,0.008) vector 2: (1,0,0,1,0,0,0,0) </code></pre> <p><code>vector 2</code> shows the membership of <code>vector 1</code> elements in specific set <strong>c</strong></p> <p>I want to implement a scoring function which would do the following steps :</p> <p>1) takes <code>vector 1</code> and <code>vector 2</code> as inputs.</p> <p>2) sort the <code>vector 1</code> with decreasing values and then sort the <code>vector 2</code> with corresponding <code>vector 1</code></p> <p>3) it's go through the sorted <code>vector 1</code> and if for the element <code>i</code> of the <code>vector 1</code> the corresponding element of sorted <code>vector 2</code> is <strong>1</strong>, then the score should be increased by <code>(m-l)</code>, else it should be decreased by <code>l</code> .</p> <p>m= length of <code>vector 1</code></p> <p>l= # of non-zero elements in <code>vector 2</code></p> <p>4) finally do the permutation on the <code>vectors 1</code> and <code>vector 2</code> and re-calculate the score of step 3. the permutation should preserve the true membership of <code>vector 1</code> element in <code>vector 2</code> . for example : <code>vector 1</code>: (10,7,4), <code>vector 2</code>: (0,0,1), after one possible permutation : <code>vector 1</code>: (4,7,10), <code>vector2</code>: (1,0,0)</p> <p>here is my attempt :</p> <pre><code> vector1&lt;- c(0.01,0.02,0.04,0.5,0.9,0.002,0.07,0.008) vector2&lt;- c(1,0,0,1,0,0,0,0) m&lt;-length(vector1) l&lt;-nnzero(vector2, na.counted = NA) score=0 score_function&lt;-function (a,b){ a&lt;-sort(a,decreasing = T) for (i in a){ if (b[i]==1) { score= + m-1 } else{ score= score-l } } score } </code></pre> <p>but I couldn't sort the <code>b</code> (vector 2) according to <code>vector 1</code> (a)</p>
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    1. USuser2806363
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    1. COCan you show us what you've already tried for this? Several of these steps are elementary (like sorting) and we need to know what level you're at with this.
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      1. USThomas
    2. COAdditionally, you don't seem to accept answers on very many of your questions. It's an important part of this site to accept answers that solve your questions.
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      1. POImplementing simple scoring function with permutation test in R
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    3. COI used sort function to sort the vector 1, but I couldn't figure out how to sort vector 2 together with vector 1 .
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      1. POImplementing simple scoring function with permutation test in R
      1. USuser2806363
 

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