README.md

In Ksieber/piccolo: Estimate Colocalization Gentic Signals

piccolo

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:

library("piccolo")
gwas_credSet <- pics.download(rsid="rs123", pvalue=-log10(1.23E-45))
eQTL_credSet <- pics.read("/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

pics.coloc:

Test for colocalization of two PICS credible sets

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

Options

|Options | Value | Default | ----------- | ---------------------------------------------------------- | ------------------ | |data1, data2 | PICS sets from pics.read or pics.download | 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

Note:

• Returns full coloc object.
• Users only need to specify the column names through pics[1|2] & rsid[1|2] if they are using credible sets that are not from pics.download().
• For "lighter" dataframe returing only H3 & H4 posteriors, use pics.coloc.lite()
• Adapted from Toby Johnson's code, which was adapted from Giambartolomei et al. 2014 colocalisation method

pics.coloc.lite:

Test for colocalization of two PICS credible sets

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

Options: Same as pics.coloc()

Note:

• Returns a "lighter" dataframe with only H3 & H4 posteriors

pics.download:

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

Example: myCredSet <- pics.download(rsid="rs6795744", pvalue = "1.23e-20")

Options:

|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

Note:

• Returns a dataframe with default colnames as pic[1|2]="PICS_probability" & rsid[1|2]="Linked_SNP" that pics.coloc anticipates as default.
• For pics.download() to work behind a proxy use this code in an R session in your ~/.Renviron. options(RCurlOptions = list(proxy="proxy.URL:PORT", proxyuserpwd="ID:PW"))

pics.read:

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

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

Known Bugs:

• If the rsID is not in the imputation used by PICs (1KGp1) then it returns the input rsID as the 1 causal SNP. This is almost certainly an erroneous credible set. This will also occur with rsIDs that do not exist. By default, pics.download() return NA.

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