View csaw user's guide

Description

Finds the location of the user's guide and opens it for viewing.

Usage

csawUsersGuide(view=TRUE)

Arguments

Details

The csaw package is designed for de novo detection of differentially bound regions from ChIP-seq data. It provides methods for window-based counting, normalization, filtering and statistical analyses via edgeR. The user guide for this package can be obtained by running this function.

For non-Windows operating systems, the PDF viewer is taken from Sys.getenv("R_PDFVIEWER"). This can be changed to x by using Sys.putenv(R_PDFVIEWER=x). For Windows, the default viewer will be selected to open the file.

Note that the user's guide is not a true vignette as it is not generated using Sweave when the package is built. This is due to the time-consuming nature of the code when run on realistic case studies.

Value

A character string giving the file location. If view=TRUE, the system's default PDF document reader is started and the user's guide is opened.

Author(s)

Aaron Lun

See Also

system

Examples

# To get the location:
csawUsersGuide(view=FALSE)
# To open in pdf viewer:
## Not run: csawUsersGuide()

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)

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(csaw)
Loading required package: GenomicRanges
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

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: 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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/csaw/csawUsersGuide.Rd_%03d_medium.png", width=480, height=480)
> ### Name: csawUsersGuide
> ### Title: View csaw user's guide
> ### Aliases: csawUsersGuide csaw
> ### Keywords: documentation
> 
> ### ** Examples
> 
> # To get the location:
> csawUsersGuide(view=FALSE)
[1] "/home/ddbj/local/lib64/R/library/csaw/doc/csawUserGuide.pdf"
> # To open in pdf viewer:
> ## Not run: csawUsersGuide()
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>