plot.MatrixEQTL
Plot histogram or QQ-plot of all p-values
Description
This method plots a histogram or QQ-plot of p-values
for all tests performed by Matrix_eQTL_engine.
Usage
## S3 method for class 'MatrixEQTL'
plot(
x,
cex = 0.5,
pch = 19,
xlim = NULL,
ylim = NULL,
main = NULL,
...)Arguments
x |
An object returned by |
cex |
A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. |
pch |
Plotting "character", i.e., symbol to use.
See |
xlim |
Set the range of the horisontal axis. |
ylim |
Set the range of the vertical axis. |
main |
Plot title. |
... |
Details
The plot type (histogram vs. QQ-plot) is determined by the
pvalue.hist parameter in the call of
Matrix_eQTL_engine function.
Value
The method does not return any value.
Note
The sample code below produces figures like these:
Histogram: 
QQ-plot: 
Author(s)
Andrey A Shabalin andrey.shabalin@gmail.com
References
The package website: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/
See Also
See Matrix_eQTL_engine for reference and sample code.
Examples
library(MatrixEQTL)
# Number of samples
n = 100
# Number of variables
ngs = 2000
# Common signal in all variables
pop = 0.2*rnorm(n)
# data matrices
snps.mat = matrix(rnorm(n*ngs), ncol = ngs) + pop
gene.mat = matrix(rnorm(n*ngs), ncol = ngs) + pop + snps.mat*((1:ngs)/ngs)^9/2
# data objects for Matrix eQTL engine
snps1 = SlicedData$new( t( snps.mat ) )
gene1 = SlicedData$new( t( gene.mat ) )
cvrt1 = SlicedData$new( )
rm(snps.mat, gene.mat)
# Slice data in blocks of 500 variables
snps1$ResliceCombined(500)
gene1$ResliceCombined(500)
# Produce no output files
filename = NULL # tempfile()
# Perform analysis recording information for a histogram
meh = Matrix_eQTL_engine(
snps = snps1,
gene = gene1,
cvrt = cvrt1,
output_file_name = filename,
pvOutputThreshold = 1e-100,
useModel = modelLINEAR,
errorCovariance = numeric(),
verbose = TRUE,
pvalue.hist = 100)
plot(meh, col="grey")
# Perform analysis recording information for a QQ-plot
meq = Matrix_eQTL_engine(
snps = snps1,
gene = gene1,
cvrt = cvrt1,
output_file_name = filename,
pvOutputThreshold = 1e-6,
useModel = modelLINEAR,
errorCovariance = numeric(),
verbose = TRUE,
pvalue.hist = "qqplot")
plot(meq)