Recommended way to subset with multiple queries?

[genomics-kl]

Hello @PoisonAlien,

Do you have a recommended way to make multiple subsets on a MAF object? I have used lapply to call subsetMaf for unique query parameters but not sure how to combine those subsetted MAF objects back into one MAF object.

Perhaps you have another suggested approach? Basically, I have a list of specific variants that I want to extract based on Chromosome, vcf_pos and Variant_Type.

Thanks!

[PoisonAlien]

Hi,
lapply or for loop, both should be fine for subsetting. However, there is no option for merging multiple MAF objects. I am happy push a function for that. I will let you know soon..

[genomics-kl]

Thanks for the prompt reply! I appreciate your adding this feature to this very useful package. In the meantime, I was able to work around this for my particular use case by chaining the unique query strings together with |. Here's an example in case this turns up in anyone's searches: "(Chromosome == 'chr7' & vcf_pos == '151859768' & Variant_Type == 'INS') | (Chromosome == 'chr7' & vcf_pos == '151962134' & Variant_Type == 'SNP')".

[PoisonAlien]

Hi,
I am glad that you figured it out. I have also pushed a function merge_mafs which takes a list of MAF objects and returns a single merged MAF. You can try it if you'd like.
Thanks for reporting. I am closing the issue, please feel to re-open if you find any issues.