piccolo: PICCOLO: Colocalization of GWAS and eQTL/pQTL signals without...

In tobyjohnson/gtx: Genetics ToolboX

Description

PICCOLO estimates the probability that two genetic signals between GWAS and e/pQTLs . are shared using colocalization approach. A proper colocalization analysis requires . full summary stats for both the GWAS and QTL studies. Unfortunately, studies frequently do not share full summary stats which makes a traditional colocalization analysis impossible.. . In this case, PICCOLO enable to do a colocalization using PICS.

Usage

piccolo(chrom, pos, rs, pval, ancestry, indication,
  dbc = getOption("gtx.dbConnection", NULL))

Arguments

chrom	SNP chromosome. Single string or vector.
pos	SNP position. Single string or vector.
rs	SNP rsid. Single string or vector.
pval	the association p-value for the SNP. Single string or vector.
ancestry	Ancestry information: EUR/ASN/AFR. Currently, only EUR is available. OPTIONAL!!
indication	Associated phenotype or trait info. OPTIONAL!!
dbc	Database connection. Default: getOption("gtx.dbConnection", NULL)

Value

a data frame containing the result of the PICS calculation.

Author(s)

Kijoung Song [e-mail]

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.