plotKdModel {scanMiR}R Documentation

plotKdModel

Description

Plots the summary of an affinity model.

Usage

plotKdModel(mod, what = c("both", "seeds", "logo"), n = 10)

Arguments

mod

A 'KdModel'

what

Either 'seeds', 'logo', or 'both' (default). 'logo' and 'both

n

The number of top 7-mers to plot (when ‘what=’seeds'')

Details

‘what=’seeds'' plots the -log(Kd) values of the top 'n' 7-mers (including both canonical and non-canonical sites), with or without the final "A" vis-a-vis the first miRNA nucleotide. ‘what=’logo'' plots a 'seqLogo' (requires the [seqLogo](https://bioconductor.org/packages/release/bioc/html/seqLogo.html) package) showing the nucleotide-wise information content and preferences for all 12-mers (centered around the seed). 'what="both"' plots both.

Value

If 'what="logo"', returns nothing a plots a position weight matrix. Otherwise returns a ggplot.

Examples

data(SampleKdModel)
plotKdModel(SampleKdModel, what="seeds")

[Package scanMiR version 0.99.26 Index]