XBSeq {XBSeq} | R Documentation

## Express function to carry out XBSeq analysis

### Description

A wrapper function to carry out XBSeq analysis procedure

### Usage

    XBSeq(counts, bgcounts, conditions, method = "pooled",
       sharingMode = "maximum", fitType = "local", pvals_only = FALSE, paraMethod='NP', big_count = 900)

### Arguments

`counts` | A data.frame or matrix contains the observed signal
`bgcounts` | A data.frame or matrix contains the background noise
`conditions` | A factor to specify the experimental design
`method` | Method used to estimate SCV
`sharingMode` | Mode of sharing of information
`fitType` | Option to fit mean-SCV relation
`pvals_only` | Logical; Specify whether to extract pvalues only
`paraMethod` | 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

This is the express function for carry out differential expression analysis. Two methods can be choosen from for `paraMethod`. '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

`estimateRealCount`, `XBSeqDataSet`, `estimateSCV`, `XBSeqTest`

### Examples

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

[Package XBSeq version 1.12.0 Index]