nullProfile: Draw a mutational profile plot

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

Draw a mutational profile plot

Description

nullProfile is a method for objects of class LowMACA that draw a barplot highlighting the significant clusters of mutations found by LowMACA statistics

Usage

nullProfile(object , conservation=NULL, windowlimits=NULL)

Arguments

object	an object of class LowMACA
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
windowlimits	A vector indicating which amino acids residues will be plotted. The vector refers to the positions in the global alignment. By default this parameter is set to NULL, that means that all the amino acids will be displayed.

Details

This method draw the second layer of the lmPlot of LowMACA. The blue dotted line is a curve that pass through all the points of the upper limit of the 95% confidence interval for the single position test performed by entropy (one point per position in the consensus). The black bars represents the density of mutations in our sample. If a bar passes the blue line, it will be depicted in orange (significant pvalue). After the correction for multiple testing, red stars appears at the top of the orange bars if a cluster is below 0.05 for the qvalue and has a conservation trident score of at least 0.1.

Value

NULL

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

lmPlot entropy

Examples

#Load homeobox example
data(lmObj)
#Calculate statistics
lmObj <- entropy(lmObj)
nullProfile(lmObj)

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