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Last data update: 2014.03.03

R: Examine the distribution of observed signal and background...

XBplot

R Documentation

Examine the distribution of observed signal and background noise

Description

Function to viewlize the distribution of observed signal X and background noise B across all genes for one specified sample

Usage

XBplot(XB, Samplenum = NULL, unit = c('counts', 'LogTPM'), Libsize = NULL, Genelength = NULL, xlab = 'log2 TPM', ylab = 'Frequencies', col = c('blue', 'red'), alpha =c(1, 0.6))

Arguments

`XB`	An XBSeqDataSet object
`Samplenum`	An integer number to specify which sample to examine
`unit`	Whether to examine the distrbution in 'counts' unit or 'LogTPM' unit. 'LogTPM' is generally recommended
`Libsize`	A single integer indicating the library size of the sample. By default, the sum of all reads mapped to exonic regions are used.
`Genelength`	A numeric vector containing genelength information. Please make sure the length and order of the gene length information is the same as arrays in the XB object.
`xlab`	lab for x axis
`ylab`	Lable for y axis
`col`	A vector of two colours for observed signal and background noise
`alpha`	A vector of two numeric numbers indicating transparency

Details

We strongly recommended users to apply XBplot to their datasets before differential expression analysis. According to our experience, for XBplot in 'logTPM' unit, the peak of distribution of background noise generally coinsides with the left hump of distribution of observed signal.

Value

Plot of distribution of observed signal and background noise.

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)
   XB <- XBSeqDataSet(Observed, Background, conditions)
   XBplot(XB, Samplenum = 1, unit = "LogTPM", Genelength = genelength[,2])

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)

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Type 'license()' or 'licence()' for distribution details.

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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/XBplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: XBplot
> ### Title: Examine the distribution of observed signal and background noise
> ### Aliases: XBplot
> 
> ### ** Examples
> 
>    conditions <- c(rep('C1', 3), rep('C2', 3))
>    data(ExampleData)
>    XB <- XBSeqDataSet(Observed, Background, conditions)
>    XBplot(XB, Samplenum = 1, unit = "LogTPM", Genelength = genelength[,2])
Warning messages:
1: In XBplot(XB, Samplenum = 1, unit = "LogTPM", Genelength = genelength[,  :
  Libsize is not provided, the sum of all the read counts that mapped to exonic
              regions in each sample is used as the total library size for that sample
2: Removed 16453 rows containing non-finite values (stat_bin). 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>