XBSeq: Express function to carry out XBSeq analysis

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

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)

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