Random sampling in R to obtain a p-value

[David O'Donnell]

Hello. I work with maize, and am using B73 ref genome v2 for my dataset. From an F2:F3 mapping population, I have identified a set of QTL for various traits. For one parent of the population, we also have identified a set of introgression regions from a wild relative. Some of the identified QTL overlap with stronger introgression regions [while others do not]. I would like to determine if the overlap is a significant effect from the wild relative, or simply due to chance.

So essentially, I believe I must perform random sampling of 'x' number of genes [total genes from introgression regions] from the genome 1000 times, and calculate each time the number of genes that overlap with QTL. Then I'd like to determine the number of times (out of 1000 random samplings) that the overlap is greater than the actual overlap [between QTL genes and introgression genes] to obtain a p-value. I know already the number of genes in QTL regions and introgression regions. My main question: Is there a simple method in R to perform the random sampling for my calculation?

Thanks!

David

[Lipps, Sarah J]

Hi David,

 

I am uncertain how to do this using r/qtl, but this can be done on the command line using the bedtools suite. More info on bedtools: https://bedtools.readthedocs.io/en/latest/

 

Cheers,

Sarah

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