MAplot: Generate maplot after differential expression test

In XBSeq: Test for differential expression for RNA-seq data

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

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.

Value

MAplot of test statistics

Author(s)

Yuanhang Liu

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)

XBSeq documentation built on Nov. 8, 2020, 11:12 p.m.