R: Function to access the dispersion estimation for each gene
dispEst
R Documentation
Function to access the dispersion estimation for each gene
Description
The dispersion estimated for each gene are stored as a data.frame after user called estimateSCV
Usage
dispEst(object, varname = NA)
dispEst(object, varname = NA) <- value
Arguments
object
XBSeqDataSet object
varname
variable name of dispersion estimates
value
The dispersion estimates for each gene
Value
A data.frame which contains the dispersion estimates for each gene
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.
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/dispEst.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dispEst
> ### Title: Function to access the dispersion estimation for each gene
> ### Aliases: dispEst dispEst,XBSeqDataSet-method dispEst<-
> ### dispEst<-,XBSeqDataSet-method
>
> ### ** Examples
>
> conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
> data(ExampleData)
> XB <- XBSeqDataSet(Observed, Background, conditions)
> XB <- estimateRealCount(XB)
> XB <- estimateSizeFactors(XB)
> XB <- estimateSCV(XB, fitType='local')
> str(dispEst(XB))
List of 1
$ disp_pooled: num [1:22609] 0.0267 0.0275 0.062 0.0337 0.0269 ...
>
>
>
>
>
> dev.off()
null device
1
>