MMDiff (version 1.8.0)

plotHistDists: plot MMD distances

Description

the generated plots are similar to MA plots, except that the computed distances (MMD) are shown on the y-axes instead of log fold change.

Usage

plotHistDists(DBA, method = "MMD", group1, group2,  field4X = "NormTotalCounts", bUsePval = FALSE, pnames = "combined", thresh = 0.05,  save2file = FALSE, fn.pics,  ftype = pdf, xlim = NULL, ylim = NULL)

Arguments

DBA

DBA object, after running compHistDists.

method

specify method used to determine distances between histograms (could be MMD, GMD or Pearson).

group1

sample ids of control group

group2

sample ids of treatment group

field4X

name of list element in DBA$MD that is used for pooling of peaks. (e.g. NormTotalCounts or RawTotalCounts)

bUsePval

logical indicating whether to use FDR (FALSE) or p-value (TRUE) for thresholding.

pnames

name of comparison used to generated p-values, eg. name1 vs name2

thresh

threshold to show significant peaks. (e.g. < 0.05)

save2file

if TRUE plot is saved to pdf file

fn.pics

file name, where the plot should be saved to.

ftype

file format for saving the plot (pdf, postcsript, png)

xlim

the x limits (x1, x2) of the plot. The default value, 'NULL', indicates that the range of the finite values to be plotted should be used.

ylim

the y limits of the plot.

See Also

getPeakProfiles, getNormFactors, compHistDists, detPeakPvals

Examples

# load DBA objects with peak profiles and pairwise distances
data(Cfp1Dists)

# determine empirical p-values:
group1 <- c("WT.AB2", "Resc.AB2")
group2 <- c("Null.AB2")
Cfp1Pvals <- detPeakPvals(Cfp1Dists, group1=group1, group2=group2,
             name1='Wt/Resc', name2='Null')

# plot distances and peaks which are significantly different:

plotHistDists(Cfp1Pvals, group1=group1, group2=group2)