landscape: Interactive 3-D association landscape for many phenotypes

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

Interactive 3-D association landscape for many phenotypes

Description

Interactive 3-D association landscape for many phenotypes

Usage

landscape(
  d,
  sliceval = 0,
  chromosome = FALSE,
  bpdivision = 1e+06,
  upperlimit = NULL,
  geneview = FALSE,
  betaplot = FALSE,
  LDblock = NULL,
  calculateLD = FALSE,
  pop = "GBR",
  R2 = 0.75,
  D = 0.75,
  mutualLD = FALSE,
  levelsdown = 0
)

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
upperlimit	Integer to indicate value of -log10(p) to do the upperlimit. If not given it will take the max -log10(p)
geneview	This checks for the common genes across the section
betaplot	This plot the beta instad of pvalue in the yaxis. The heat map layer is based on the pvalue.
LDblock	If want to pass a custom LDblock file for division of BP groups (applicable only for chromosomal level)
calculateLD	This shoudld be set to true if the calcualte LD logic needed to be added to the plot
pop	The population to select for calculation the LD (default GB)
R2	The value to set to calculate LD
D	THe value to set to calcualte LD
mutualLD	Calcualte the mutual LD SNP between the phenotypes
levelsdown	Used to find the independant signals chromosoem view the max peak is selected

Author(s)

George Gittu

Examples

## Not run: 
x <- list(hdl,ldl,trig,tchol)
phenos <- c("HDL","LDL","TRIGS","TOTALCHOLESTROL")
y <- processphegwas(x, phenos)
## pass the dataframe from the processphegwas

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

# Showing only the crusts above a certain threshold
landscape(y,sliceval = 6)

# 3D landscape visualization of chromosome number 16
landscape(y,sliceval = 6,chromosome = 16)

# 3D landscape visualization of chromosome number 16, with bp division on 1,000,000
landscape(y,sliceval = 6,chromosome = 16,bpdivision = 1000000)
landscape(y,sliceval = 6,chromosome = 16,bpdivision = 1000000, betaplot = TRUE)

## End(Not run)

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