landscapetable: 3-D association table for many phenotypes

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

3-D association table for many phenotypes

Description

3-D association table for many phenotypes

Usage

landscapetable(d, sliceval = 8, chromosome = 1, 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
chromosome	Integer to indicate the chromosome number thats interested, If not given entire chromosome is given
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.