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POR: t-test over all subsets over all columns
 

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  1. POR: t-test over all subsets over all columns
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    <p>This is a follow up question from <a href="https://stackoverflow.com/q/9661469/612191">R: t-test over all columns</a></p> <p>Suppose I have a huge data set, and then I created numerous subsets based on certain conditions. The subsets should have the same number of columns. Then I want to do t-test on two subsets at a time (outer loop) and then for each combination of subsets go through all columns one column at a time (inner loop).</p> <p>Here is what I have come up with based on previous answer. This one stops with an error.</p> <pre><code>C &lt;- c("c1","c1","c1","c1","c1", "c2","c2","c2","c2","c2", "c3","c3","c3","c3","c3", "c4","c4","c4","c4","c4", "c5","c5","c5","c5","c5", "c6","c6","c6","c6","c6", "c7","c7","c7","c7","c7", "c8","c8","c8","c8","c8", "c9","c9","c9","c9","c9", "c10","c10","c10","c10","c10") X &lt;- rnorm(n=50, mean = 10, sd = 5) Y &lt;- rnorm(n=50, mean = 15, sd = 6) Z &lt;- rnorm(n=50, mean = 20, sd = 5) Data &lt;- data.frame(C, X, Y, Z) Data.c1 = subset(Data, C == "c1",select=X:Z) Data.c2 = subset(Data, C == "c2",select=X:Z) Data.c3 = subset(Data, C == "c3",select=X:Z) Data.c4 = subset(Data, C == "c4",select=X:Z) Data.c5 = subset(Data, C == "c5",select=X:Z) Data.Subsets = c("Data.c1", "Data.c2", "Data.c3", "Data.c4", "Data.c5") library(plyr) combo1 &lt;- combn(length(Data.Subsets),1) adply(combo1, 1, function(x) { combo2 &lt;- combn(ncol(Data.Subsets[x]),2) adply(combo2, 2, function(y) { test &lt;- t.test( Data.Subsets[x][, y[1]], Data.Subsets[x][, y[2]], na.rm=TRUE) out &lt;- data.frame("Subset" = rownames(Data.Subsets[x]), , "Row" = colnames(x)[y[1]] , "Column" = colnames(x[y[2]]) , "t.value" = round(test$statistic,3) , "df"= test$parameter , "p.value" = round(test$p.value, 3) ) return(out) } ) } ) </code></pre>
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    1. USery
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    1. COLook at `str(Data.Subsets)`.
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      1. USjoran
    2. COIt's not entirely clear what you want your code to do. Do you mean perform a test between c1 in subset 1 and c1 in subset 2 followed by a t test on c2 in subset 1 and c2 in subset 2 etc? At a quick glance your Data.Subsets is just a character vector. It doesn't actually contain any of the dataframe subsets you've made. so using looping over it does nothing because you want to deal with dataframes and you are passing your code strings.
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      1. USDavy Kavanagh
    3. CO@DavyKavanagh: Yes, the Data.Subsets is just a character vector. I tried to use as.data.frame to convert it to a dataframe, but with the same result. What I wanted to do is: to capture these data subset names, and access the actual data subsets in the loop. I guess the pertinent question is: how to pass the dataframe as a parameter in the loop?
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