Hi,
Is there a package/function to generate random genomic position in R ? If not it's not complicated to write something using sample() but I do not want to re-re-re-reinvent the wheel ..
Edit : I wrote that. Some benchmarking with other given solutions in this thread seems to be required !
generateRandomPos <- function(n,chr,chr.sizes,width=1){
random_chr <- sample(x=chr,size=n,prob=chr.sizes,replace=T)
random_pos <- sapply(random_chr,function(chrTmp){sample(chr.sizes[chr==chrTmp],1)})
res <- GRanges(random_chr,IRanges(random_pos,random_pos+width))
return(res)
}
Thanks
I don't think there is a function for it already, but I suggest you to get chromosome lengths from the TxDb.Hsapiens.UCSC.hg19.knownGene object from Homo.sapiens.
> library(Homo.sapiens)
> seqlengths(TxDb.Hsapiens.UCSC.hg19.knownGene)[1:24]
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8
249250621 243199373 198022430 191154276 180915260 171115067 159138663 146364022
chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16
141213431 135534747 135006516 133851895 115169878 107349540 102531392 90354753
chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY
81195210 78077248 59128983 63025520 48129895 51304566 155270560 59373566
> rr = data.frame(chr=sample(seqlevels(TxDb.Hsapiens.UCSC.hg19.knownGene)[1:24], 40, replace=F))
> rr$start = apply(rr, 1, function(x) {
round(runif(1, 0, seqlengths(TxDb.Hsapiens.UCSC.hg19.knownGene)[x][[1]]), 0) }
)
> rr$end = rr$start + runif(1, 1, 1000) # random intervals of 1-1000 bases
> rr$strand = sample(c("+", "-"))
> rr.gr = makeGRangesFromDataFrame(rr)
> rr.gr
GRanges object with 40 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [225055397, 225056035] +
[2] chr12 [125243701, 125244339] -
[3] chr22 [ 42744305, 42744943] +
[4] chr1 [ 79241981, 79242619] -
[5] chr7 [151649796, 151650434] +
... ... ... ...
[36] chr21 [33907192, 33907830] -
[37] chr18 [73931535, 73932173] +
[38] chrY [14300243, 14300881] -
[39] chr17 [26049438, 26050076] +
[40] chr22 [26631730, 26632368] -
-------
Is there a way to make random genomic ranges, but avoiding overlap between the segments? I want to randomly place non-overlapping segments (with a given length[width]) across the genome. Thanks.
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(Davetang is the author from gist.github.com/davetang/6548010):
In fact it's not really random as
my_random_chr[i] <- sample(x=my_chr,size=1)will pick a chromosome unregarding of its size. Anyway thank you I'll will rewrite the code for my usage and post it here ;)Nice but I don't like the for loop. It would be easy and much more elegant to convert it to a function and apply.
I wrote that : chr= chromosome names and chr.sizes = their associated size
You need a random position .may be with sample(1:length sequence,1,true) will gives one sample
what about bedtools
[shuffle][1]. You can take a look at this link as well. Ideally they allow to pick up regions from the original master file. I guess you can also use this code to generate one.