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Last data update: 2014.03.03

R: Express function to carry out XBSeq analysis

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')

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

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.

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(XBSeq)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

    Welcome to 'XBSeq'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XBSeq/XBSeq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: XBSeq
> ### Title: Express function to carry out XBSeq analysis
> ### Aliases: XBSeq
> 
> ### ** Examples
> 
>    conditions <- c(rep('C1', 3), rep('C2', 3))
>    data(ExampleData)
>    Stats <- XBSeq(Observed, Background, conditions)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>