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.

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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

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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

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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

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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"))

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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")

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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.