R: Plot histogram or QQ-plot of all p-values

Description

This method plots a histogram or QQ-plot of p-valuesfor all tests performed by Matrix_eQTL_engine.

Usage

## S3 method for class 'MatrixEQTL'
plot(x, cex = 0.5, pch = 19, xlim = NULL, ylim = NULL,...)

Arguments

`x`	An object returned by `Matrix_eQTL_engine`.
`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 `points`.
`xlim`	Set the range of the horisontal axis.
`ylim`	Set the range of the vertical axis.
`...`	further graphical parameters passed to `lines` and `points`.

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 Shabalin ashabalin@vcu.edu

References

The package website: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

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)

Plot histogram or QQ-plot of all p-values