MAplot.bioCond {MAnorm2} | R Documentation |
Create an MA Plot on Two bioCond
Objects
Description
Given two bioCond
objects, the function draws an MA plot,
which is a scatter plot with signal intensity differences between the two
conditions against the average signal intensities across conditions.
Usage
## S3 method for class 'bioCond'
MAplot(
x,
y,
col = NULL,
pch = NULL,
ylim = c(-6, 6),
xlab = "A value",
ylab = "M value",
plot.legend = TRUE,
...
)
Arguments
x , y |
Two |
col , pch |
Optional length-4 vectors specifying the colors and point characters of 4 types of genomic intervals: common peak regions, peak regions specific to the 2nd condition, peak regions specific to the 1st condition, and the others. Elements are recycled if necessary. |
ylim |
A length-two vector specifying the plotting range of Y-axis
(i.e., the M value). Each M value falling outside the range will be
shrunk to the corresponding limit. Setting the option to |
xlab , ylab |
Labels for the X and Y axes. |
plot.legend |
A logical value indicating whether to add a legend. |
... |
Further arguments to be passed to |
Details
Genomic intervals are classified based on
the occupancy
field in each of
the two bioCond
objects. See bioCond
for a full
description of the structure of a bioCond
object.
Value
The function returns NULL
.
Note
While it's not strictly required, ChIP-seq samples contained in the
two bioCond
objects are expected to have been normalized
prior to calling this function. These samples could be normalized all
together before being classified into biological conditions (via
normalize
). Alternatively, normalization can also be
performed at the level of bioCond
objects (via
normBioCond
).
Given the typically large number of points to draw, you may want to
use alpha
to adjust color transparency if you
intend to specify col
explicitly.
See Also
bioCond
for creating a bioCond
object;
MAplot.default
for producing an MA plot on normalized
signal intensities of two ChIP-seq samples; normalize
for
performing an MA normalization on ChIP-seq samples;
normBioCond
for normalizing a set of bioCond
objects.
Examples
data(H3K27Ac, package = "MAnorm2")
attr(H3K27Ac, "metaInfo")
## Create MA scatter plots for the comparisons between individuals.
# Perform the MA normalization and construct bioConds to represent
# individuals.
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)
# MA plots on pairs of individuals.
MAplot(conds[[1]], conds[[2]], main = "GM12890 vs. GM12891")
abline(h = 0, lwd = 2, lty = 5)
MAplot(conds[[1]], conds[[3]], main = "GM12890 vs. GM12892")
abline(h = 0, lwd = 2, lty = 5)
MAplot(conds[[2]], conds[[3]], main = "GM12891 vs. GM12892")
abline(h = 0, lwd = 2, lty = 5)