landscapefulltable: 3-D association table for many phenotypes(entire genome)

In georgeg0/PheGWAS: R package to do many-variant many-phenotype association

3-D association table for many phenotypes(entire genome)

Description

3-D association table for many phenotypes(entire genome)

Usage

landscapefulltable(d, sliceval = 6, bpdivision = 1e+06)

Arguments

d	DataFrame output from processphegwas
sliceval	Integer to indicate value of -log10(p) to do the sectionalcut. Usually value > -log10 6 is considered to be significant
bpdivision	Integer value to indicate the base pair divisions. By default it is 100,000 bp. This vis only applciable on a single chromosome view. For entire chromosoem view the max peak is selected

Author(s)

George Gittu

Examples

## Not run: 
# table of chromosome number 16, with bp division on 1,000,000 (default is 1,000,000)
x <- list(hdl,ldl,trig,tchol)
phenos <- c("HDL","LDL","TRIGS","TOTALCHOLESTROL")
y <- processphegwas(x, phenos)
landscapetable(y,sliceval = 6,chromosome = 16,bpdivision = 1000000)

## End(Not run)

georgeg0/PheGWAS documentation built on Oct. 15, 2022, 7:49 a.m.