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)

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

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

### 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 1.18.0 Index]