doc/PheGWAS-vignette.R

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

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

## ----setup---------------------------------------------------------------
library(PheGWAS)

## ------------------------------------------------------------------------
head(hdl)

## ------------------------------------------------------------------------
head(ldl)

## ------------------------------------------------------------------------
head(trig)

## ------------------------------------------------------------------------
head(tchol)

## ------------------------------------------------------------------------
head(bmimen)

## ------------------------------------------------------------------------
head(bmiwomen)

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

## ------------------------------------------------------------------------
y <- processphegwas(x,phenos)

## ------------------------------------------------------------------------
landscape(y)

## ------------------------------------------------------------------------
landscape(y,sliceval = 10)

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

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

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

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

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