protter: Draw a Protter plot

In ste-depo/LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Draw a Protter plot

Description

This is a wrapper around Protter web service for LowMACA class objects that draw a protter style plot.

Usage

protter(object, filename = "protter.png", threshold = 0.05 , conservation=NULL)

Arguments

object	an object of class LowMACA
filename	a character string that identifies the file name where protter plot will be stored. Default "protter.png"
threshold	a numeric value in the interval (0 , 1] that identifies the significant mutations. Default 0.05
conservation	a numeric value in the range of 0-1 that defines the threshold of trident conservation score to include the specified position. The default value is inherited from the slot entropy, whose default is 0.1

Details

Using the information in the slot alignment, a request is send to Protter server. Protter will predict a possible sencondary structure for the consensus sequence (if possible) and highlights the significant clusters of mutations found by LowMACA (if any). A significant pvalue is colored in orange, a significant qvalue is colored in red.

Value

NULL

Author(s)

Stefano de Pretis , Giorgio Melloni

References

Protter website

See Also

LowMACA-class entropy

Examples

#Load homeobox example
data(lmObj)
#Calculate statistics
lmObj <- entropy(lmObj)
#Create protter.png
protter(lmObj)

ste-depo/LowMACA documentation built on Oct. 15, 2022, 11:53 p.m.