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hansenlab / RecountGenotyper

Genotype calling from Recount3 RNA-seq data.
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Add snps_gr example file #9

Open caalo opened 1 year ago

caalo commented 1 year ago

It's great that you have test.bw and test.csv.zst in the package to give the user a demo. Can you add a GRanges file for snps_gr variable in GetMandS() function so that I can run through the Example you wrote for GetMandS() without an error?

caalo commented 1 year ago

Oh, I see that if snps_gr=NULL the argument value, then it will try to download the snps_gr file. However, the file https://livejohnshopkins-my.sharepoint.com/:u:/r/personal/arazi2_jh_edu/Documents/RecountGenotyper/biallelic_SNP_gr.rds?csf=1&web=1&e=glKCqA link is broken.

Let's find a place to host the SNPs and model file!!

There is also a issue in the example documentation -- you have:

test_geno<-GetMandS(snps_gr, bigWig_path, alt_path, sample_id_rep, temp_folder=tempdir())

it should be 

 test_geno<-GetMandS(snps_gr=NULL, bigWig_path, coverage_cutoff=4, alt_path, sample_id_rep, temp_folder= tempdir())

because you want the user to use the default snps_gr, and by not saying anything about coverage_cutoff you shift all the arguments one over. Usually, when you have arguments that have a default value such as snps_gr and coverage_cutoff, you should have them to be the last arguments to prevent confusion. (this might be a bad habit carry-over from my own code.)