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POlapply and data.frame in R
 

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    <p>I am attempting to use R to accept as many user input files as required and to take those files and make one histogram per file of the values stored in the 14th column. I have gotten this far:</p> <pre><code>library("tcltk") library("grid") File.names&lt;-(tk_choose.files(default="", caption="Choose your files", multi=TRUE, filters=NULL, index=1)) Num.Files&lt;-NROW(File.names) test&lt;-sapply(1:Num.Files,function(x){readLines(File.names[x])}) data&lt;-read.table(header=TRUE,text=test[1]) names(data)[14]&lt;-'column14' dat &lt;- list(file1 = data.frame("column14"), file2 = data.frame("column14"), file3 = data.frame("column14"), file4 = data.frame("column14")) #Where the error comes up tmp &lt;- lapply(dat, `[[`, 2) lapply(tmp, function(x) {hist(x, probability=TRUE, main=paste("Histogram of Coverage")); invisible()}) layout(1) </code></pre> <p>My code hangs up though on the line that states <code>tmp &lt;- lapply(dat,</code>[[<code>, 2)</code> The error that comes up is one of two things. If the line reads as above then the error is this: </p> <pre><code>Error in .subset2(x, i, exact = exact) : subscript out of bounds Calls: lapply -&gt; FUN -&gt; [[.data.frame -&gt; &lt;Anonymous&gt; </code></pre> <p>I did some research and found that it could be caused by a double [[]] so I changed it to <code>tmp &lt;- lapply(dat,</code>[<code>, 2)</code> to see if it would do any good (as many tutorials said it might) but that just resulted in this error: </p> <pre><code>Error in `[.data.frame`(X[[1L]], ...) : undefined columns selected Calls: lapply -&gt; FUN -&gt; [.data.frame </code></pre> <p>The input files all will follow this pattern:</p> <pre><code>Targ cov av_cov 87A_cvg 87Ag 87Agr 87Agr 87A_gra 87A%_1 87A%_3 87A%_5 87A%_10 87A%_20 87A%_30 87A%_40 87A%_50 87A%_75 87A%_100 1:028 400 0.42 400 0.42 1 1 2 41.8 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1:296 400 0.42 400 0.42 1 1 2 41.8 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 </code></pre> <p>Is this a common problem? Can anyone explain it to me? I am not too familiar with R but I hope to continue learning. Thanks EDIT: For reproducibility, if I run:</p> <pre><code>head(test) head(data) x &lt;- list(mtcars, mtcars, mtcars);lapply(x, head) head(dat) </code></pre> <p>This is the result:</p> <pre><code> &gt; head(test) [,1] [1,] "Targ cov av_cov 87A_cvg 87Ag 87Agr 87Agr 87A_gra 87A%_1 87A%_3 87A%_5 87A%_10 87A%_20 87A%_30 87A%_40\t87A%_50\t87A%_75\t87A%_100" [2,] "1:028 400\t0.42\t400\t0.42\t1\t1\t2\t41.8\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0" [3,] "1:296 400\t0.42\t400\t0.42\t1\t1\t2\t41.8\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0" [4,] "1:453 1646\t8.11\t1646\t8.11\t7\t8\t13\t100.0\t100.0\t87.2\t32.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0" [5,] "1:427 1646\t8.11\t1646\t8.11\t7\t8\t13\t100.0\t100.0\t87.2\t32.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0" [6,] "1:736 5105\t29.68\t5105\t29.68\t14\t29\t48\t100.0\t100.0\t100.0\t86.0\t65.7\t49.4\t35.5\t16.9\t0.0\t0.0" &gt; head(data) [1] Targ cov av_cov X87A_cvg X87Ag X87Agr X87Agr.1 [8] X87A_gra X87A._1 X87A._3 X87A._5 X87A._10 X87A._20 X87A._30 [15] X87A._40 X87A._50 X87A._75 X87A._100 &lt;0 rows&gt; (or 0-length row.names) &gt; x &lt;- list(mtcars, mtcars, mtcars);lapply(x, head) [[1]] mpg cyl disp hp drat wt qsec vs am gear carb Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 [[2]] mpg cyl disp hp drat wt qsec vs am gear carb Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 [[3]] mpg cyl disp hp drat wt qsec vs am gear carb Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 &gt; head(dat) $file1 X.column14. 1 column14 $file2 X.column14. 1 column14 $file3 X.column14. 1 column14 $file4 X.column14. 1 column14 &gt; tmp &lt;- lapply(dat, `[`, 2) Error in `[.data.frame`(X[[1L]], ...) : undefined columns selected Calls: lapply -&gt; FUN -&gt; [.data.frame Execution halted </code></pre>
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    1. COIt's probably a very simple fix, however, without reproducible data we can't really help easily. You can take care of this by using `lapply(dat, head)`. Using `mtcars` it would work like this: `x <- list(mtcars, mtcars, mtcars);lapply(x, head)`. That will allow us to know what `dat` looks like and how to best provide assistance. For more direction on making a reproducible example please see: http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
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      1. USTyler Rinker
    2. COTry to inspect the value of `dat` immediately after you define it. You'll notice it's not what you expect it to be. Use `str(dat)` or `head(dat)` to do this.
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    3. CO@TylerRinker I added information to help make it reproducible
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