XBSeqTest {XBSeq} | R Documentation

## XBSeq test for differential expression

### Description

The same method is adopted from DESeq for testing differential expression

### Usage

    XBSeqTest(XB, condA, condB, pvals_only = FALSE, method = c("NP", "MLE"), big_count = 900)

### Arguments

`XB` | A XBSeqDataSet object
`condA` | Factor level specified for condition A
`condB` | Factor level specified for condition B
`pvals_only` | Logical;whether or not only extract p values
`method` | method to use for estimation of distribution parameters, 'NP' or 'MLE'. See details section for details
`big_count` | An integer specify a count number above which where be considerred as 'big' and beta approximation will be used instead for testing differential expression

### Details

Differential expression analysis based on statistical methods proposed for DESeq. Details about the method can be found in DESeq manual page. Two methods can be choosen from for `method`. 'NP' stands for non-parametric method. 'MLE' stands for maximum liklihood estimation method. 'NP' is generally recommended for experiments with replicates smaller than 5.

### Value

A data.frame with following columns:

`id` | rownames of XBSeqDataSet
`baseMean` | The basemean for all genes
`baseMeanA` | The basemean for condition 'A'
`baseMeanB` | The basemean for condition 'B'
`foldChange` | The fold change compare condition 'B' to 'A'
`log2FoldChange` | The log2 fold change
`pval` | The p value for all genes
`padj` | The adjusted p value for all genes

### 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

`XBSeq`, `estimateSCV`

### Examples

       data(ExampleData)
       conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
       XB <- XBSeqDataSet(Observed, Background, conditions)
       XB <- estimateRealCount(XB)
       XB <- estimateSizeFactors(XB)
       XB <- estimateSCV(XB)
       Teststas <- XBSeqTest(XB, levels(conditions)[1L], levels(conditions)[2L])
       str(Teststas)

[Package XBSeq version 1.20.0 Index]