plot.aovBioCond {MAnorm2} | R Documentation |
Plot an aovBioCond
Object
Description
Given an aovBioCond
object, which records the results of
calling differential genomic intervals across a set of bioCond
objects, this method creates a scatter plot of
(conds.mean, log10(between.ms))
pairs from all genomic intervals,
marking specifically the ones that show a statistical significance. See
aovBioCond
for a description of the two variables and the
associated hypothesis testing. The mean-variance curve associated with the
bioCond
objects is also added to the plot, serving as a baseline to
which the between.ms
variable of each interval could be compared.
Usage
## S3 method for class 'aovBioCond'
plot(
x,
padj = NULL,
pval = NULL,
col = alpha(c("black", "red"), 0.04),
pch = 20,
xlab = "Mean",
ylab = "log10(Var)",
args.legend = list(x = "bottomleft"),
args.lines = list(col = "green3", lwd = 2),
...
)
Arguments
x |
An object of class |
padj , pval |
Cutoff of adjusted/raw p-value for selecting
significant intervals. Only one of the two arguments is effectively
used; |
col , pch |
Optional length-2 vectors specifying the colors and point characters of non-significant and significant intervals, respectively. Elements are recycled if necessary. |
xlab , ylab |
Labels for the X and Y axes. |
args.legend |
Further arguments to be passed to
|
args.lines |
Further arguments to be passed to
|
... |
Further arguments to be passed to
|
Value
The function returns NULL
.
See Also
bioCond
for creating a bioCond
object;
fitMeanVarCurve
for fitting a mean-variance curve for
a set of bioCond
objects; aovBioCond
for
calling differential intervals across multiple bioCond
s.
Examples
data(H3K27Ac, package = "MAnorm2")
attr(H3K27Ac, "metaInfo")
## Call differential genomic intervals among GM12890, GM12891 and GM12892
## cell lines and visualize the overall analysis results.
# Perform MA normalization and construct bioConds to represent the cell
# lines.
norm <- normalize(H3K27Ac, 4, 9)
norm <- normalize(norm, 5:6, 10:11)
norm <- normalize(norm, 7:8, 12:13)
conds <- list(GM12890 = bioCond(norm[4], norm[9], name = "GM12890"),
GM12891 = bioCond(norm[5:6], norm[10:11], name = "GM12891"),
GM12892 = bioCond(norm[7:8], norm[12:13], name = "GM12892"))
autosome <- !(H3K27Ac$chrom %in% c("chrX", "chrY"))
conds <- normBioCond(conds, common.peak.regions = autosome)
# Variations in ChIP-seq signals across biological replicates of a cell line
# are generally of a low level, and their relationship with the mean signal
# intensities is expected to be well modeled by the presumed parametric
# form.
conds <- fitMeanVarCurve(conds, method = "parametric", occupy.only = TRUE)
summary(conds[[1]])
plotMeanVarCurve(conds, subset = "occupied")
# Perform a moderated ANOVA on these cell lines.
res <- aovBioCond(conds)
head(res)
# Visualize the overall analysis results.
plot(res, padj = 1e-6)