qqplot | R Documentation |
Functions for visualizing association test results by means of a quantile-quantile (Q-Q) plot
## S4 method for signature 'AssocTestResultRanges,missing' qqplot(x, y, xlab=deparse(substitute(x)), ylab=deparse(substitute(y)), common.scale=TRUE, preserveLabels=FALSE, lwd=1, lcol="red", ..., conf.level=NULL, conf.args=NULL) ## S4 method for signature 'AssocTestResultRanges,AssocTestResultRanges' qqplot(x, y, xlab=deparse(substitute(x)), ylab=deparse(substitute(y)), common.scale=TRUE, preserveLabels=FALSE, lwd=1, lcol="red", ..., conf.level=NULL, conf.args=NULL)
x,y |
objects of class
|
xlab |
if |
ylab |
if |
common.scale |
if |
preserveLabels |
if |
lwd |
line width for drawing the diagonal line which theoretically corresponds to the equality of the two distributions; if zero, no diagonal line is drawn. |
lcol |
color for drawing the diagonal line |
conf.level |
dummy argument for compatibility with the new version of the function in the stats package; currently unused |
conf.args |
dummy argument for compatibility with the new version of the function in the stats package; currently unused |
... |
all other arguments are passed to
|
If qqplot
is called for an
AssocTestResultRanges
object without specifying the second argument y
,
a Q-Q plot of the raw p-values in x
against a uniform
distribution of expected p-values is created, where the theoretical
p-values are computed using the ppoints
function.
In this case, the log-transformed observed p-values contained in x
are plotted on the vertical axis and the log-transformed expected
p-values are plotted
on the horizontal axis. If preserveLabels
is TRUE
,
xlab
and ylab
are used as axis labels as usual.
However, if preserveLabels
is FALSE
, which is the
default, xlab
is interpreted as object label for x
, i.e.
the object whose p-values are plotted on the vertical axis.
If qqplot
is called for two
AssocTestResultRanges
object x
and
y
, the log-transformed raw p-values of x
and y
are plotted against each other, where the p-values of x
are plotted on
the horizontal axis and the p-values of x
are plotted on the
vertical axis.
like the standard qqplot
function from
the stats package, qqplot
returns an invisible list
containing the two sorted vectors of p-values.
Ulrich Bodenhofer bodenhofer@bioinf.jku.at
http://www.bioinf.jku.at/software/podkat
AssocTestResultRanges
## load genome description data(hgA) ## partition genome into overlapping windows windows <- partitionRegions(hgA) ## load genotype data from VCF file vcfFile <- system.file("examples/example1.vcf.gz", package="podkat") Z <- readGenotypeMatrix(vcfFile) ## read phenotype data from CSV file (continuous trait + covariates) phenoFile <- system.file("examples/example1lin.csv", package="podkat") pheno <-read.table(phenoFile, header=TRUE, sep=",") ## train null model with all covariates in data frame 'pheno' nm.lin <- nullModel(y ~ ., pheno) ## perform association tests res.p <- assocTest(Z, nm.lin, windows, kernel="linear.podkat") res.s <- assocTest(Z, nm.lin, windows, kernel="linear.SKAT") ## plot results qqplot(res.p) qqplot(res.p, res.s, xlab="PODKAT results", ylab="SKAT results") qqplot(res.p, res.s, xlab="PODKAT results", ylab="SKAT results", preserveLabels=TRUE) qqplot(res.p, res.s, common.scale=FALSE)
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