MAplot.diffBioCond: Create an MA Plot on Results of Comparing Two 'bioCond'...

In MAnorm2: Tools for Normalizing and Comparing ChIP-seq Samples

Create an MA Plot on Results of Comparing Two bioCond Objects

Description

This method produces an MA plot demonstrating the results of comparing two bioCond objects. More specifically, it draws a scatter plot consisting of the genomic intervals having been compared, and those intervals with differential ChIP-seq signals between the two conditions are explicitly indicated.

Usage

## S3 method for class 'diffBioCond'
MAplot(
  x,
  padj = NULL,
  pval = NULL,
  col = alpha(c("black", "red"), 0.1),
  pch = 20,
  ylim = c(-6, 6),
  xlab = "A value",
  ylab = "M value",
  args.legend = list(x = "topright"),
  ...
)

Arguments

x	An object of class "diffBioCond", typically obtained by passing two bioCond objects to diffTest.
padj, pval	Cutoff of adjusted/raw p-value for selecting differential intervals. Only one of the two arguments is effectively used; pval is ignored if padj is specified. The default is equivalent to setting padj to 0.1.
col, pch	Optional length-2 vectors specifying the colors and point characters of non-differential and differential intervals, respectively. 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 NULL to suppress this behavior.
xlab, ylab	Labels for the X and Y axes.
args.legend	Further arguments to be passed to legend.
...	Further arguments to be passed to plot.

Value

The function returns NULL.

See Also

bioCond for creating a bioCond object; fitMeanVarCurve for fitting a mean-variance curve given a list of bioCond objects; diffTest for making a comparison between two bioCond objects; alpha for adjusting color transparency.

Examples

data(H3K27Ac, package = "MAnorm2")
attr(H3K27Ac, "metaInfo")

## Make a comparison between GM12891 and GM12892 cell lines and create an MA
## plot on the comparison results.

# Perform MA normalization and construct bioConds to represent the two cell
# lines.
norm <- normalize(H3K27Ac, 5:6, 10:11)
norm <- normalize(norm, 7:8, 12:13)
conds <- list(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 differential tests between the two cell lines.
res <- diffTest(conds[[1]], conds[[2]])
head(res)

# Visualize the overall test results.
MAplot(res, padj = 0.001)
abline(h = 0, lwd = 2, lty = 5, col = "green3")

MAnorm2 documentation built on Oct. 29, 2022, 1:12 a.m.