plot Peak

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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

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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

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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)