biomaRt user guide has an example which appears a bit more straightforward.
What is the underlying resource? dbSNP?
Need to reconcile possible differences between GRCh37 and hg19?
My understanding is that with hg38, GRCh38 = hg38 so that isn't an issue?
Would it be best to put the onus on the user to find GRanges of the SNPs (and possibly wider blacklisted loci) and simply have that as an argument? The function becomes much simpler, but we should still have some documentation for how such a GRanges object might be built.
Function call
filter_loci_by_snps(bs, ...?)
Description
Used after bsseq::read.bismark and before or after filter_loci_by_coverage() to remove loci that contain C to T or G to A SNPs because these are confounding for bisulfite conversion.
Arguments
bs a BSseq object that hasn't been subjected to tile_by_windows() or tile_by_regions().
...?
Values
A BSseq object where loci with C/T or G/A SNPs removed.
Tests
Test that SNPs are removed in the destranded and stranded case. This will require slightly altering the test data from #28 to include a SNP or more.
Issues to resolve before implementation
GRangesof the SNPs (and possibly wider blacklisted loci) and simply have that as an argument? The function becomes much simpler, but we should still have some documentation for how such aGRangesobject might be built.Function call
filter_loci_by_snps(bs, ...?)Description
Used after
bsseq::read.bismarkand before or afterfilter_loci_by_coverage()to remove loci that contain C to T or G to A SNPs because these are confounding for bisulfite conversion.Arguments
bsaBSseqobject that hasn't been subjected totile_by_windows()ortile_by_regions().Values
A
BSseqobject where loci with C/T or G/A SNPs removed.Tests
Test that SNPs are removed in the destranded and stranded case. This will require slightly altering the test data from #28 to include a SNP or more.