plotDists: plotDists

In dhelekal/mmdiff3: Statistical Testing for ChIP-Seq data sets

Description

scatterplot showing distances between peaks

Usage

plotDists(MD, dist.method = "MMD", whichContrast = 1, which.group1 = NULL,
  which.group2 = NULL, diff.method = "MMD.locfit", bUsePval = FALSE,
  th = 0.1, title = NULL, what = 3, xlim = NULL, ylim = NULL,
  xlog10 = TRUE, Peak.IDs = NULL, withLegend = TRUE,
  shiny_df_opt = FALSE)

Arguments

MD	DBAmmd Object. This Object can be created using DBAmmd().
dist.method	specify method used for distances between samples. Currently only Maximum Mean Discrepancy (MMD) and Kolmogorov-Smirnov (KS) implemented. (DEFAULT: 'MMD')
whichContrast	index determining which of the set contrast should be used. (DEFAULT: 1)
which.group1	subset samples from group1 (DEFAULT: NULL)
which.group2	subset samples from group2 (DEFAULT: NULL)
diff.method	which method to use to determine significant peaks (DEFAULT: 'MMD.locfit')
bUsePval	if TRUE p-values instead of FDRs are used (DEFAULT: FALSE)
th	significance threshold for differential called peaks (DEFAULT: 0.1)
title	an overall title for the plot (DEFAULT: NULL)
what	which dists to overlay: 1: only between group distances, 2: between and within group distances, 3: between and within group distances, and significant peaks highlightend (DEFAULT: 3)
xlim	specify x range (DEFAULT: NULL)
ylim	specify y range (DEFAULT: NULL)
xlog10	should x range be plotted in log10 scale (DEFAULT: TRUE)
Peak.IDs	Highlight specific subset of peaks (DEFAULT: NULL)
withLegend	(DEFAULT: TRUE)
shiny_df_opt	Option returns a dataframe for shiny (DEFAULT: FALSE)

Examples

data("MMD")
plotDists(MMD, whichContrast=1)

dhelekal/mmdiff3 documentation built on July 25, 2019, 8:18 p.m.