epiMA: Make MA Plot

In TheJacksonLaboratory/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

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, pointsize = 1.5)

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)
pointsize	A numeric value to adjust point size (default: 1.5)

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, pointsize = 1.5)

TheJacksonLaboratory/epihet documentation built on Dec. 22, 2020, 1:10 p.m.