PatternHeatmap: Generate a Heatmap of patterns in DNA sequence
In heatmaps: Flexible Heatmaps for Functional Genomics and Sequence Features

Description Usage Arguments Value Methods (by class) See Also Examples

Generate a Heatmap of patterns in DNA sequence

PatternHeatmap(seq, pattern, ...)

## S4 method for signature 'DNAStringSet,character'
PatternHeatmap(seq, pattern, coords = NULL,
  min.score = NULL, label = NULL)

## S4 method for signature 'DNAStringSet,matrix'
PatternHeatmap(seq, pattern, coords = NULL,
  min.score = "80%", label = NULL)

`seq`	A DNAString of equal length
`pattern`	A nucleotide pattern or PWM
`...`	additional arguments used by methods This function creates a Heatmap from a set of DNA sequences. The resulting heatmap will be binary, with 1 representing a match and 0 otherwise. Patterns can be specified as a character vectore, eg. "CTCCC", or as a PWM. These arguments are passed to Biostrings functions, 'vmatchPattern' and 'matchPWM'. Character arguments can contain standard ambiguity codes. PWMs must be 4 by n matricies with columns names ACGT. "min.score" is specified either as an absolute value, or more commonly as a percentage e.g. "80 for details. PatternHeatmaps often look much better after smoothing.
`coords`	Co-ordinates for the heatmap, defaults to c(0, width(windows))
`min.score`	Minimum score for PWM match
`label`	Label for the heatmap

A heatmap

seq = DNAStringSet,pattern = character: Heatmap of sequence patterns from sequence and character
seq = DNAStringSet,pattern = matrix: Heatmap of sequence patterns from sequence and matrix

smoothHeatmap

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data(HeatmapExamples)
PatternHeatmap(string_set, "TA", coords=c(-100, 100), label="TA")
PatternHeatmap(string_set, tata_pwm, coords=c(-100, 100), min.score="80%", label="TATA PWM")

Attaching package: 'heatmaps'

The following object is masked from 'package:base':

    scale

coords: -100 100 
nseq: 500 
obs: 100000 
scale: 0 1 
label: TA 
coords: -100 100 
nseq: 500 
obs: 100000 
scale: 0 1 
label: TATA PWM