A variable contained in design(ecs). The expression
values will be fitted to this variable using the the formula
" ~ fitExpToVar * exon".
denominator
A value of the sample annotation (e.g. condition) to use as a denominator
in the log2 fold change. As a default, the function will take
the annotation of the first sample.
BPPARAM
A "BiocParallelParam" instance.
See ?bplapply for details.
maxRowsMF
For the exon fold change estimation, the size of the model matrix
for the fitted glm increases with the number of samples and
the number of exons for a specific gene (see the DEXSeq paper
for details). Since the glm fit for big models is very slow,
the maxRowsMF parameter allows to set a threshold on the number
of rows from the model matrix (the number of rows of the model
matrix will be number of samples times the number of exons of a
gene). For all genes passing this threshold, the exon fold
changes will be estimated by fitting a slightly different
but equivalent model. The formula remains the same, but instead
of fitting one model per gene that considers all its exons, it
considers, for each exon, the counts from the specific exon and
the sum of the rest of exons of the same gene.
independentFiltering
Logical indicating whether independent filtering should be
applied automatically. For the exons that were discarded,
fold changes won't be estimated.
filter
A vector of filter statistics over which the independent
filtering will be optimized. The default is the normalized
exon means.
Details
Exon usage coefficients are calculated by fitting
a GLM from the joint data of all exons of the same gene.
The model frame can be found in the slot object@modelFrameBM
of a DEXSeqDataSet object. The model
'~ fitExpToVar * exon' is fitted.
The resulted coefficients are arranged and reformatted
in order to remove gene expression effects, leaving only exon
usage effects for each individual exon in each level of
'fitExpToVar'. These values are used by the function
plotDEXSeq. For specific details please check
the DEXSeq paper.
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(DEXSeq)
Loading required package: BiocParallel
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: DESeq2
Loading required package: AnnotationDbi
Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DEXSeq/estimateExonFoldChanges.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estimateExonFoldChanges
> ### Title: Estimates exon usage coefficients from the fitted terms of the
> ### GLM.
> ### Aliases: estimateExonFoldChanges
>
> ### ** Examples
>
> data(pasillaDEXSeqDataSet, package="pasilla")
> dxd <- estimateSizeFactors( dxd )
> dxd <- estimateDispersions( dxd )
using supplied model matrix
using supplied model matrix
> dxd <- testForDEU( dxd )
using supplied model matrix
> dxd <- estimateExonFoldChanges( dxd )
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.