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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",fig.width=12, fig.height=9, message=FALSE, tidy=TRUE, dpi=75)

library(PheGWAS)

Following processed summary data are from the lipid consortium:

head(hdl)

head(ldl)

head(trig)

head(tchol)

The dataframe’s are passed to processphegwas function as a list of dataframe’s.

x <- list(hdl,ldl,trig,tchol)
phenos <- c("HDL","LDL","TRIGS","TOTALCHOLESTROL")

This preprocess the dataframes’ for passing to the landscape function.

y <- processphegwas(x,phenos)

3D landscape visualization of all the phenotypes across the base pair #positions

landscape(y)

3D landscape visualization of all the phenotypes across the base pair #positions, showing only the crusts above a certain threshold

landscape(y,sliceval = 10)

3D landscape visualization of all the phenotypes across the base pair #positions, showing only the crusts that are within a certain region (between sliceval and upperlimit)

landscape(y,sliceval = 10 ,chromosome = 19,upperlimit = 50)

3D landscape visualization of chromosome number 16, with bp division on #1,000,000 (default is 1,000,000)

landscape(y,sliceval = 7.5,chromosome = 19)

3D landscape visualization of chromosome number 16, with bp division on #1,000,000. Gene View is active

landscape(y,sliceval = 7.5,chromosome = 19, geneview = TRUE)

Effect size plot

landscape(y,sliceval = 7.5,chromosome = 16,bpdivision = 1000000, betaplot = TRUE)

3D visualization with LD block (for european population) passing externally, parameter to pass LD and also calculate the mutualLD block

landscape(y, sliceval = 30, chromosome = 19,bpdivision= 1000000,calculateLD= TRUE,mutualLD = TRUE)

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