XBSeq (version 1.2.2)

XBplot: 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

Value

Plot of distribution of observed signal and background noise.

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.

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

ExampleData

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])