plot.eqtl | R Documentation |
The function offers informative plots for an eqtl
object.
## S3 method for class 'eqtl'
plot(x, file = NULL, which = NULL, sig = 0.01, verbose = TRUE,
centered = TRUE, log = FALSE, mc.cores = 1, genome = NULL, ...)
x |
Object of class |
file |
Store set of graphics under that file name. |
which |
Specifies for which genes should the plot be created. |
sig |
Chosen significance level. |
verbose |
Logical, extended feedback of the function. |
centered |
Logical, plot should be centered around center gene. |
log |
Logical, y-axis scale is log(base=10)-scaled. |
mc.cores |
Amount of cores for parallel computing. |
genome |
The name of an existing genome. |
... |
Additional plotting parameters. |
This function plots the test results of an eqtl
object. Typically is the tested gene in the center and the p-values of associated SNPs are visualized.
Monomorphic SNPs and those that were missing are separately plotted. Test results that are smaller than the value given to sig
are marked in red.
The y.axis can be switched to log10 scale by setting the logical parameter log=TRUE
in that case are bars instead of dots plotted. If the y-axis is on log-scale
it is also possible to give a second eqtl
object to the function and plot the test results for both.
The annotation feature is currently under development and only available in limited form.
An eQTL plot
Daniel Fischer
# Load the data
data("annotTrack")
data("geneEXP")
data("genotData")
## Not run:
# A cis eQTL for 10 different genes:
EQTL1 <- eQTL(gex=geneEXP[,1:10] , xAnnot = annotTrack,
geno= genotData)
# A trans-eQTl for two different genes:
EQTL2 <- eQTL(gex=geneEXP[,c(1,1000)] , xAnnot = annot.bed,
geno= genotData, windowSize = NULL)
# Visualize the second cis-eQTL:
plot(EQTL1, which=2)
# Visualize the trans-eQTL
plot(EQTL2)
## End(Not run)
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