PatternHeatmap {heatmaps}R Documentation

Generate a Heatmap of patterns in DNA sequence

Description

Generate a Heatmap of patterns in DNA sequence

Usage

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)

Arguments

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

Value

A heatmap

Methods (by class)

See Also

smoothHeatmap

Examples

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")

[Package heatmaps version 1.8.0 Index]