Filter function to mark C/T and G/A SNPs

[rcavalcante]

Issues to resolve before implementation

• Which Bioconductor SNP resource to use?
  • SNPlocs.Hsapiens.dbSNP144.GRCh37 is possible, but the API for extracting C/T and G/A SNPs is not clear to me yet.
  • 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.