GEO_boxplot.MA: quick way to draw a boxplot for specified contrast via MAList...

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

boxplot.MA is based on boxplot.genedata2 and a quick way to draw a boxplot for specified contrast via MAList object.boxplot.MA2() is based on boxplot.MA and appropriate for multiple significant markers plotting.

Usage

boxplot.MA(MA1,
           design,
           matrix.type="M",
           contrast,
           select,
           p.val.matrix,
           p.val.col="P.Value",
           p.val.position=NULL)

boxplot.MA2(MA1,
            matrix.type="M",
            cut.n,
            design,
            contrast,
            p.val.matrix,
            p.val.col="P.Value",
            p.val.position=NULL,
            names="test1")

Arguments

MA1	MA object after lucky::MApipeline2()
design	a design matrix from model.matrix()
matrix.type	M or A matrix
contrast	the group in every facet
select	marker names
p.val.matrix	a result object containing p.val
p.val.col	colnames of p value in the p.val.matrix
p.val.position	the position of significant symbol in the plot

Author(s)

Weibin Huang

Examples

boxplot.MA(MA1,
           design,
           matrix.type="M",
           contrast=c("Np","N0"),
           select=sig.genes,
           p.val.matrix=sig.expr,
           p.val.col="P.Value",
           p.val.position=NULL)

boxplot.MA(MA1,
           design,
           matrix.type="A",
           contrast=c("Np","N0"),
           select=sig.genes,
           p.val.matrix=sig.expr,
           p.val.col="P.Value",
           p.val.position=NULL)

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.