plotPeak: plot Peak

In MMDiff2: Statistical Testing for ChIP-Seq data sets

Description

This function plots histograms of fragment positions over a pre defined regions of interests / peaks. Can also show occurences of Sequence motifs and annotated objects (e.g. genes).

Usage

plotPeak(MD, Peak.id, Sample.ids = NULL, NormMethod = NULL,
  plot.input = FALSE, whichPos = "Center", whichContrast = NULL,
  Motifs = NULL, Motifcutoff = "80%", anno = NULL, xaxt = NULL,
  xlim = NULL, ylim = NULL)

Arguments

MD	DBAmmd Object. This Object can be created using DBAmmd().
Peak.id	Peak id to specify which Peak to plot. (coresponding to names of Regions(MD))
Sample.ids	which samples to draw. If NULL all samples are drawn. (DEFAULT: NULL)
NormMethod	whether to apply normailzation factors. currently no normalization method implemented (DEFAULT: None)
plot.input	whether to plot input controls (DEFAULT: TRUE)
whichPos	specifies which relative positions of mapped fragments should to be considered. Can be one of: 'Left.p', 'Right.p', 'Right.p' and 'Left.n': Start and end positions of fragments mapping to positive or negative strand, respectively ('Right.p' and 'Left.n' are not available for single-end reads). Additionally inferred positions: 'Center.n','Center.p','Center','Left','Right'. (DEFAULT: 'Center')
whichContrast	index determining which of the set contrast should be used. (DEFAULT: 1)
Motifs	TF binding sites (DEFAULT: NULL)
Motifcutoff	(Default: "80%")
anno	either a GRanges objects containing annotated objects, e.g. genes, or a list of GRanges Objects. (Default: NULL)
xaxt	(Default: NULL)
xlim	(Default: NULL)
ylim	(Default: NULL)

Examples

dev.off()
data("MMD")
plotPeak(MMD,Peak.id='6',plot.input=FALSE)

# add annotation (Overlapping genes)
data("mm9-Genes")
GR <- list(UCSCKnownGenes = GR)
plotPeak(MMD, Peak.id='6', plot.input = FALSE, anno=GR)

# add TF binding sites
library('MotifDb')
motifs <- query(query(MotifDb, 'Mmusculus'), 'E2F')
plotPeak(MMD, Peak.id='6', plot.input = FALSE,
       Motifs=motifs,Motifcutoff="80%")

# split peaks by contrast
plotPeak(MMD, Peak.id='6', plot.input = FALSE, whichContrast=1,
       Motifs=motifs,Motifcutoff="80%",anno=GR)

MMDiff2 documentation built on Nov. 8, 2020, 11:03 p.m.