<p>Is it because rand.gr has not been initialised, so when you ask to set rand.gr[i] it can't because there isn't one yet?</p>

<p>If you set i to a value (e.g. 1), and run the lines inside your loop, which of the lines produces the error?</p>

<p>If you don't need to retain all the random genomic ranges at the end, you could just leave out some of the [i]s, something like this:</p>

<pre><code>for(i in 1:ncol(rand.df)){
  rand.gr &lt;- gr[(elementMetadata(gr)[,"gene"] %in% rand.df[,i])]
  dists &lt;- distanceToNearest(x = rand.gr)
  output &lt;- print(mcols(dists[,1]))
}
</code></pre>

CC BY-SA 4.0
2019-11-08T12:38:31.643Z
Isn't `output` being overwritten with each iteration?
haci
CC BY-SA 4.0
2019-11-08T13:17:33.080Z
Thanks, I do need a file with essentially columns of distance data (each column corresponding to a column in rand.df)
R-MASHup
CC BY-SA 4.0
2019-11-08T13:23:18.570Z
this seemed to create another problem: https://www.dropbox.com/s/jl03i9nm87vwbxz/Screenshot%202019-11-08%20at%2013.21.04.png?dl=0
R-MASHup
CC BY-SA 4.0
2019-11-12T10:38:51.643Z
haci is correct, ouput is overwritten on each time round the loop.
Jay Moore
CC BY-SA 4.0
2019-11-08T11:47:10.547Z
2019-11-08T12:17:14.480Z
2019-11-08T12:17:14.480Z
Jay Moore
<p>You could do this much more easily and much faster on the command line, starting with an unsorted BED file of genes called <code>genes.unsorted.bed</code>:</p>

<pre><code>$ sort-bed genes.unsorted.bed | shuf - | head -5 - | sort-bed - | closest-features --closest --dist --no-overlaps - &gt; answer.bed
</code></pre>

<p>Replace the <code>5</code> in <code>head -5</code> with however many random genes you want. Remove <code>--no-overlaps</code> if you want to allow consideration of overlapping genes (which returns a distance of zero).</p>

<p>Output columns are delimited with <code>|</code>. This can be replaced with another delimiter, but the output can be brought into R easily with <code>read.table</code> or similar.</p>

<p>Ref: <a href="https://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html" rel="nofollow noreferrer">https://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html</a></p>

CC BY-SA 4.0
2019-11-15T23:08:15.010Z
i thought closest-features requires a reference and an input file?
R-MASHup
CC BY-SA 4.0
2019-11-12T23:29:49.513Z
2019-11-12T23:29:49.513Z
Alex Reynolds
<p>I want to compute the nearest neighbour distances using a for loop. I can do this with a random subset by doing this:</p>

<pre><code>df &lt;-  read.table("tmp.txt", header=F)
colnames(df) &lt;- c("gene", "seqnames", "start", "stop", "LOCID")
gr &lt;- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)

# genes of interest in a list
gene.list &lt;- read.table("careplastic_diffs.txt")

# filters the GenomicRanges object with genes of interest
sub.gr &lt;- gr[(elementMetadata(gr)[, "gene"] %in% gene.list$V1)]

# compute distances
dists &lt;- distanceToNearest(x = sub.gr)

mcols(dists)[,1] # contains a list of distances
</code></pre>

<p>I now want to essentially do this 5 times, using the same logic as above:</p>

<pre><code>## create a rand dataframe, each column is a random list of 50 genes
rand.df &lt;- data.frame(replicate(5, sample(gene.list$V1, 50)))

# loop through columns and gets distances and prints to a file
for(i in 1:ncol(rand.df)){
  rand.gr[i] &lt;- gr[(elementMetadata(gr)[,"gene"] %in% rand.df[,i])]
  dists[i] &lt;- distanceToNearest(x = rand.gr[i])
  output &lt;- print(mcols(dists[i][,1]))
}
</code></pre>

<p>But I can't seem to make this work.</p>

<blockquote>
  <p>Error: subscript contains out-of-bounds indices In addition: Warning
  message: In recycleSingleBracketReplacementValue(value, x, nsbs) :<br>
  number of values supplied is not a sub-multiple of the number of
  values to be replaced</p>
</blockquote>

<p>It's probably something really silly but any help would be appreciated ... </p>

<r><bioconductor><genomicranges><genomefeatures>
GenomicRanges: get nearest neighbor distances for random genes using a for loop
# GenomicRanges: get nearest neighbor distances for random genes using a for loop

(Asked by: username_0 on 2019-11-08)

I want to compute the nearest neighbour distances using a for loop. I can do this with a random subset by doing this:
df <-  read.table("tmp.txt", header=F)
colnames(df) <- c("gene", "seqnames", "start", "stop", "LOCID")
gr <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)

# genes of interest in a list
gene.list <- read.table("careplastic_diffs.txt")

# filters the GenomicRanges object with genes of interest
sub.gr <- gr[(elementMetadata(gr)[, "gene"] %in% gene.list$V1)]

# compute distances
dists <- distanceToNearest(x = sub.gr)

mcols(dists)[,1] # contains a list of distances

I now want to essentially do this 5 times, using the same logic as above:
## create a rand dataframe, each column is a random list of 50 genes
rand.df <- data.frame(replicate(5, sample(gene.list$V1, 50)))

# loop through columns and gets distances and prints to a file
for(i in 1:ncol(rand.df)){
  rand.gr[i] <- gr[(elementMetadata(gr)[,"gene"] %in% rand.df[,i])]
  dists[i] <- distanceToNearest(x = rand.gr[i])
  output <- print(mcols(dists[i][,1]))
}

But I can't seem to make this work.

Error: subscript contains out-of-bounds indices In addition: Warning
  message: In recycleSingleBracketReplacementValue(value, x, nsbs) :
  number of values supplied is not a sub-multiple of the number of
  values to be replaced

It's probably something really silly but any help would be appreciated ...

**Tags:** r, bioconductor, genomicranges, genomefeatures

---

## 2 answers

### Answer by username_1 on 2019-11-08. Score: 1 | Accepted answer

Is it because rand.gr has not been initialised, so when you ask to set rand.gr[i] it can't because there isn't one yet?
If you set i to a value (e.g. 1), and run the lines inside your loop, which of the lines produces the error?
If you don't need to retain all the random genomic ranges at the end, you could just leave out some of the [i]s, something like this:
for(i in 1:ncol(rand.df)){
  rand.gr <- gr[(elementMetadata(gr)[,"gene"] %in% rand.df[,i])]
  dists <- distanceToNearest(x = rand.gr)
  output <- print(mcols(dists[,1]))
}

> **Comments:**
> **username_2**: Isn't `output` being overwritten with each iteration?  
> **username_0**: Thanks, I do need a file with essentially columns of distance data (each column corresponding to a column in rand.df)  
> **username_0**: this seemed to create another problem: https://www.dropbox.com/s/jl03i9nm87vwbxz/Screenshot%202019-11-08%20at%2013.21.04.png?dl=0  
> **username_1**: haci is correct, ouput is overwritten on each time round the loop.  

---

### Answer by username_3 on 2019-11-12. Score: 0

You could do this much more easily and much faster on the command line, starting with an unsorted BED file of genes called genes.unsorted.bed:
$ sort-bed genes.unsorted.bed | shuf - | head -5 - | sort-bed - | closest-features --closest --dist --no-overlaps - > answer.bed

Replace the 5 in head -5 with however many random genes you want. Remove --no-overlaps if you want to allow consideration of overlapping genes (which returns a distance of zero).
Output columns are delimited with |. This can be replaced with another delimiter, but the output can be brought into R easily with read.table or similar.
Ref: https://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html

> **Comments:**
> **username_0**: i thought closest-features requires a reference and an input file?  

---

