pics_calc: PICS calculation using the linkage information of 10,000 UKB...
In tobyjohnson/gtx: Genetics ToolboX

Description Usage Arguments Details Value Author(s)

The PICS algorithm calculates the most likely causal SNPs given the observed association signal . at a locus. For an associated locus, enter the most highly-associated SNP (referred to as the index SNP) and the strength of association. Using the linkage information in 10,000 UKB samples, the algorithm identifies the SNPs that are most likely to be the causal variants responsible for the association (PICS_Probability).

1	pics_calc(index.data, dbc = getOption("gtx.dbConnection", NULL))

`dbc`	Database connection. Default: getOption("gtx.dbConnection", NULL)
`data`	Data frame with columns rs\|chr:pos, pval, ancestry and indication. Use the same column names for your data. However, ancestry and indication are optional.

See Genetic and Epigenetic Fine-Mapping of Causal Variants in Autoimmune Disease by Kyle Kai-How Farh,et al. Nature 518, 337–343 (19 February 2015) at http://www.nature.com/nature/journal/v518/n7539/full/nature13835.html#close

a data frame containing the result of the PICS calculation.

Kijoung Song kys21207@gsk.com

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