aba.zoom: aba.zoom - A function to help zoom in on specific data from...
In tobyjohnson/gtx: Genetics ToolboX

Description Usage Arguments Details Author(s) Examples

This function is to enable users to zoom in on specific features from the aba coloc data. The default aba plots can be very large and messy, and filtering these data can be difficult. To enable users to filter the data, this function will help "zoom" in on specific features such as genes or GWAS. This function can be used 1-2 times depending on the desired level of zoom.

1	aba.zoom(.data, hgncid, entity, analysis2, p12_ge = 0.8)

`hgncid`	HGNC symbol.
`entity`	Typically ensemblid.
`analysis2`	GWAS analysis ID
`p12_ge`	[Default >= 0.80] This is the "H4" posterior probability cutoff

Tier 1 zoom: All colocs for the input query, all genes with shared coloc traits (extended gene list), and all non-shared traits for the extended gene list.

Tier 2 zoom: All colocs for the input query, all genes with shared colocs. Excludes non-shared traits from the extended gene list. Note, Tier 2 zoom does not always further resolve data complexity.

Karsten Sieber karsten.b.sieber@gsk.com

Use aba.wrapper to run query and get data. 
colocs <- aba.wrapper(hgncid = "HMGCR", neale_only = TRUE, protein_coding_only = TRUE)

Tier 1 zoom
colocs %>% pluck("data", 1) %>% aba.zoom(hgncid = "HMGCR") %>% aba.plot()

Tier 2 zoom:
colocs %>% pluck("data", 1) %>% aba.zoom(hgncid = "HMGCR") %>% aba.zoom(hgncid = "HMGCR") %>% aba.plot()