MAplot {XBSeq} | R Documentation

## 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

### 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)

[Package XBSeq version 1.12.0 Index]