PatternHeatmap: Generate a Heatmap of patterns in DNA sequence

In mgperry/heatmaps: Flexible Heatmaps for Functional Genomics and Sequence Features

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 on the difference between the minimum and maximum scores, not between zero and the maximum score, since it is based on the log odds ratio. As of Bioconductor 3.5, this behaviour is different to the 'matchPWM' function in Biostrings. 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")

mgperry/heatmaps documentation built on May 22, 2019, 8:53 p.m.