pics.coloc: pics.coloc : Test for colocalization of two PICS sets Adapted...

In Ksieber/piccolo: Estimate Colocalization Gentic Signals

Description

pics.coloc : Test for colocalization of two PICS sets Adapted from [Toby Johnson's code](https://github.com/tobyjohnson/gtx/blob/master/R/abf.R "Toby's coloc in R") Which was adapted from [Giambartolomei et al. 2014](https://www.ncbi.nlm.nih.gov/pubmed/24830394 "Giambartolomei et al. 2014") colocalization method

Usage

pics.coloc(data1, data2, pics1 = "PICS_probability",
  pics2 = "PICS_probability", rsid1 = "Linked_SNP", rsid2 = "Linked_SNP",
  rounded = 6, priorc1 = 1e-04, priorc2 = 1e-04, priorc12 = 1e-05)

Arguments

data1	PICS sets, from pics.read or pics.download
data2	PICS sets, from pics.read or pics.download
pics1	Column name to pull PICS prob from data1 if data not from pics.* Default = "PICS_probability"
pics2	Column name to pull PICS prob from data2 if data not from pics.* Default = "PICS_probability"
rsid1	Column name to pull rsid from if data not from pics.* Default = "Linked_SNP"
rsid2	Column name to pull rsid from if data not from pics.* Default = "Linked_SNP"
rounded	[#] Decimal points to round posteriors to
priorc1	Prior probability for colocalization with siganl for data1 Default = 1e-4
priorc2	Prior probability for colocalization with siganl for data2 Default = 1e-4
priorc12	Prior probability for colocalization of both signals. Default = 1e-5

Value

Full colocalization info. For concise dataframe returing *only* H3 & H4 posteriors use pics.coloc.lite()

Examples

myColoc <- pics.coloc(gwas.credSet, eQTL.credSet)

Ksieber/piccolo documentation built on Jan. 11, 2020, 11:39 a.m.