This code enables users to get PICS credible sets for nearly any index SNP with a pvalue. Users can then test if two genetic signals colocalize in a Bayesian framework.

Example workflow:

gwas_credSet <-"rs123", pvalue=-log10(1.23E-45))
eQTL_credSet <-"/full/path/to/pics.txt")
myColoc      <- pics.coloc(gwas_credSet, eQTL_credSet)

See the pinned issue for a pptx showing further illustrating an example. Also available here


Test for colocalization of two PICS credible sets

Example: myColoc <- pics.coloc(gwas_credSet, eQTL_credSet)


|Options | Value | Default | ----------- | ---------------------------------------------------------- | ------------------ | |data1, data2 | PICS sets from or | NA |pics1, pics2 | column name to pull PICS prob from. | "PICS_probability" |rsid1, rsid2 | column name to pull rsid from. | "Linked_SNP" |rounded | [#] Decimal points to round posteriors to. | |priorc1 | Prior probability for a siganl in data1 | 1e-4 |priorc2 | Prior probability for a siganl in data2 | 1e-4 |priorc12 | Prior probability for colocalization of both signals. | 1e-5



Test for colocalization of two PICS credible sets

Example: myColoc <- pics.coloc.lite(gwas_credSet, eQTL_credSet)

Options: Same as pics.coloc()


Query the PICs website and get a PICs credible set for a SNP of interest

Example: myCredSet <-"rs6795744", pvalue = "1.23e-20")


|Options | Value | Default | --------- | ------------------------------------------------ | ----------------------------------- | |rsid | SNP rsID | Example: "rs1234" |pvalue | pvalue or -log10(pvalue). | Examples: -log10(1.23E-45) or 45 |ancestry | [EUR, ASN, AFR] | "EUR" |output | Full path and name for the download to be saved. | held in memory


Load a PICs file that was either download from the website (copy+paste to a text file) or a saved output from

Example: myCredSet <-"/full/path/to/PICs_credSet.txt")

Known Bugs:

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