XBSeq (version 1.2.2)

MAplot: Generate maplot after differential expression test

Description

Generate maplot after differential expression test based on ggplot2

Usage

MAplot(stats, ylim, padj = TRUE, pcuff = 0.1, lfccuff = 1,  linecol = "red3", xlab = "mean of normalized counts", ylab = expression(log[2] ~ fold ~ change), shape)

Arguments

stats

The output of XBSeqTest

ylim

Range of limit for y axis

padj

Whether to use adjusted p value or not

pcuff

Threshold for pvalue

lfccuff

Log fold change cutoff

linecol

Colour of horizontal line

xlab

Lable for x axis

ylab

Lable for y axis

shape

The shape of the points used

Value

MAplot of test statistics

Details

Generate classic MAplot for DE analysis using ggplot2, where A and M are from slot baseMean and slot log2FoldChange of the test statistics aftering calling XBSeqTest. The ggplot2 package generally generate figures of better quality as well as give user better control of the plotting system compared with the base plotting system.

References

H. I. Chen, Y. Liu, Y. Zou, Z. Lai, D. Sarkar, Y. Huang, et al., "Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads," BMC Genomics, vol. 16 Suppl 7, p. S14, Jun 11 2015.

See Also

XBSeqTest

Examples

   conditions <- c(rep('C1', 3), rep('C2', 3))
   data(ExampleData)
   Stats <- XBSeq(Observed, Background, conditions)
   MAplot(Stats)