epiMA {epihet}R Documentation

Make MA Plot

Description

Creates an MA plot from the differential heterogeneity data calculated from the diffHet() function. For each loci, graphs the average of both group means on the x-axis and the heterogeneity difference on the y-axis. Graphs coordinates with significant adjusted p-values in red.

Usage

epiMA(pval.matrix, padjust.cutoff = 0.05, pch = ".", sve = FALSE)

Arguments

pval.matrix

The data frame returned from the diffHet() function that contains means, p-values, adjusted p-values, and heterogeneity difference

padjust.cutoff

The adjusted p-value cutoff to confirm a significant value. (default: 0.05)

pch

The plotting character to be used in the MA plot (default: '.')

sve

A boolean to save the plot (default: FALSE)

Value

A figure

Examples

diff.het.matrix<-data.frame(chromosome=c(rep("1",10)),
loci=paste("loci",seq_len(10),sep="-"),subtype.mean=c(0.21,0.23,0.37,0.26,
0.29,0.31,0.29,0.13,0.12,0.093),Normal.mean=c(0.01,0.01,0.01,0.02,
0.02,0.01,0.01,0.79,0.73,0.79),het.dif=c(0.20,0.220,0.360,0.240,0.270,
0.300,0.280,-0.660,-0.610,-0.697),p.value=c(3.08e-03,1.43e-02,9.27e-03,
3.45e-02,2.99e-02,3.68e-02, 4.60e-02, 5.65e-10, 9.18e-10,
9.98e-11),p.adjust=c(8.84e-03,2.76e-02, 2.04e-02, 5.01e-02,
4.56e-02, 5.24e-02, 6.08e-02, 3.74e-08, 5.22e-08,
1.06e-08),type=rep("pdr",10))

epiMA(pval.matrix = diff.het.matrix, padjust.cutoff = 0.05,
pch = ".", sve = TRUE)

[Package epihet version 1.4.0 Index]