makeXmatrix: Create design matrix

In Senbee/Sequgio: Isoform expression estimation based on RNA-seq data

Description

Extract useful information from an annotation file to create design matrix used in expression estimation.

Usage

makeXmatrix(object,method=c("SE","PE"),mulen,verbose=FALSE,mcpar,...)

Arguments

object	An object of class GRangesList as returned by reshapeTxDb
method	Specify what method to use, if a design matrix structure for "single end" ("SE") or "paired-end" ("PE") library. Defualts to "SE"
mulen	Numeric. And estimate of average fragment length
verbose	verbose output. Defaults to no messages.
mcpar	An object of (virtual) class "BiocParallelParam" specifying parameters for parallel computing using BiocParallel
...	Additional arguments for specific methods

Value

A list containing the design matrix for each unit

Author(s)

Stefano Calza <[e-mail]>, Chen Suo, Agus Salim and Yudi Pawitan

References

Suo C, Calza S, Salim A, Pawitan Y. Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. Bioinformatics. 2014 Feb 15;30(4):506-13

See Also

getCounts, fitModels

Examples

data("TxDb")
param = SerialParam()
Design <- makeXmatrix(txdb[1:5],method="PE",mulen=200,mcpar=param)

Senbee/Sequgio documentation built on May 9, 2019, 1:21 p.m.