lmPlotSingleSequence: Draw a LowMACA comprehensive plot of a specified gene within...

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

Draw a LowMACA comprehensive plot of a specified gene within a LowMACA object

Description

LowMACA comprehensive plot is a four layers plot that summarize the entire LowMACA output

Usage

lmPlotSingleSequence(object , gene , mail=NULL , perlCommand="perl")

Arguments

object	a LowMACA class object
gene	a Gene Symbol that identifies one of the gene analyzed in the LowMACA object
mail	if not NULL, it must be a valid email address to use EBI clustalo web service. Default is to use a local clustalo installation
perlCommand	a character string containing the path to Perl executable. if missing, "perl" will be used as default. Only used in web mode

Details

If the specified gene has more than one domain of the same type and mode is pfam, the plot is composed by four layers:

1. The bar plot visualized by bpAll

2. The distribution of mutations against the 95% confidence interval superior limit of the null hypothesis (dotted line) with orange bars representing a position with a pvalue <0.05 and a red star for qvalue<0.05

3. The Trident score distribution

4. The logo plot representing the consensus sequence

If the specified gene has only one domain of the same type and mode is pfam, the plot is composed by two layers:

1. The bar plot visualized by bpAll

2. The distribution of mutations against the 95% confidence interval superior limit of the null hypothesis (dotted line) with orange bars representing a position with a pvalue <0.05 and a red star for qvalue<0.05

If mode is gene, the plot is composed by three layers:

1. The bar plot visualized by bpAll

2. The Pfam domains structure inside the protein

3. The distribution of mutations against the 95% confidence interval superior limit of the null hypothesis (dotted line) with orange bars representing a position with a pvalue <0.05 and a red star for qvalue<0.05

Value

NULL

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

lmPlot bpAll

Examples

#Load homeobox example and draw the plot
data(lmObj)
#DUXA has a significant cluster of mutation
#Plot Mutations on DUXA gene in the 
#original sequences of its domains PF00046
lmPlotSingleSequence(lmObj , gene="DUXA")

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