Read SMC files

Description

This function reads in SMCs (simple molecular concepts) from individual text files.

Usage

readSmc(files)

Arguments

Value

A list of SMC objects

Author(s)

Kyle Furge <kyle.furge@vai.org> and Karl Dykema <karl.dykema@vai.org>

References

??

See Also

writeSmc

Examples

datadir <- system.file("extdata", package = "PGSEA")
sample <- readGmt(file.path(datadir, "sample.gmt"))
str(sample)
sample[[1]]@reference <- "fileName"

## Not run: 
	writeSmc(sample[[1]])
	smc <- readSmc("fileName-0.txt")

## End(Not run)

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)

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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(PGSEA)
Loading required package: GO.db
Loading required package: AnnotationDbi
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

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")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Loading required package: annaffy
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PGSEA/readSmc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readSmc
> ### Title: Read SMC files
> ### Aliases: readSmc smc-class
> ### Keywords: data
> 
> ### ** Examples
> 
> 
> 
> datadir <- system.file("extdata", package = "PGSEA")
> sample <- readGmt(file.path(datadir, "sample.gmt"))
> str(sample)
List of 6
 $ ras UP - pmid: 16273092   NA :Formal class 'smc' [package "PGSEA"] with 10 slots
  .. ..@ reference : chr "ras UP - pmid: 16273092  "
  .. ..@ desc      : chr "NA "
  .. ..@ source    : chr(0) 
  .. ..@ design    : chr(0) 
  .. ..@ identifier: chr(0) 
  .. ..@ species   : chr(0) 
  .. ..@ data      : chr(0) 
  .. ..@ private   : chr(0) 
  .. ..@ creator   : chr(0) 
  .. ..@ ids       : chr [1:181] "101" "154" "384" "490" ...
 $ ras DN - pmid: 16273092   NA :Formal class 'smc' [package "PGSEA"] with 10 slots
  .. ..@ reference : chr "ras DN - pmid: 16273092  "
  .. ..@ desc      : chr "NA "
  .. ..@ source    : chr(0) 
  .. ..@ design    : chr(0) 
  .. ..@ identifier: chr(0) 
  .. ..@ species   : chr(0) 
  .. ..@ data      : chr(0) 
  .. ..@ private   : chr(0) 
  .. ..@ creator   : chr(0) 
  .. ..@ ids       : chr [1:69] "19" "604" "834" "835" ...
 $ myc UP - pmid: 16273092   NA :Formal class 'smc' [package "PGSEA"] with 10 slots
  .. ..@ reference : chr "myc UP - pmid: 16273092  "
  .. ..@ desc      : chr "NA "
  .. ..@ source    : chr(0) 
  .. ..@ design    : chr(0) 
  .. ..@ identifier: chr(0) 
  .. ..@ species   : chr(0) 
  .. ..@ data      : chr(0) 
  .. ..@ private   : chr(0) 
  .. ..@ creator   : chr(0) 
  .. ..@ ids       : chr [1:106] "219" "471" "617" "1019" ...
 $ myc DN - pmid: 16273092   NA :Formal class 'smc' [package "PGSEA"] with 10 slots
  .. ..@ reference : chr "myc DN - pmid: 16273092  "
  .. ..@ desc      : chr "NA "
  .. ..@ source    : chr(0) 
  .. ..@ design    : chr(0) 
  .. ..@ identifier: chr(0) 
  .. ..@ species   : chr(0) 
  .. ..@ data      : chr(0) 
  .. ..@ private   : chr(0) 
  .. ..@ creator   : chr(0) 
  .. ..@ ids       : chr [1:89] "27" "101" "406" "493" ...
 $ 5p   NA                      :Formal class 'smc' [package "PGSEA"] with 10 slots
  .. ..@ reference : chr "5p  "
  .. ..@ desc      : chr "NA "
  .. ..@ source    : chr(0) 
  .. ..@ design    : chr(0) 
  .. ..@ identifier: chr(0) 
  .. ..@ species   : chr(0) 
  .. ..@ data      : chr(0) 
  .. ..@ private   : chr(0) 
  .. ..@ creator   : chr(0) 
  .. ..@ ids       : chr [1:136] "2533" "345557" "90268" "6389" ...
 $ 5q   NA                      :Formal class 'smc' [package "PGSEA"] with 10 slots
  .. ..@ reference : chr "5q  "
  .. ..@ desc      : chr "NA "
  .. ..@ source    : chr(0) 
  .. ..@ design    : chr(0) 
  .. ..@ identifier: chr(0) 
  .. ..@ species   : chr(0) 
  .. ..@ data      : chr(0) 
  .. ..@ private   : chr(0) 
  .. ..@ creator   : chr(0) 
  .. ..@ ids       : chr [1:640] "30832" "404734" "2554" "2559" ...
> sample[[1]]@reference <- "fileName"
> 
> ## Not run: 
> ##D 	writeSmc(sample[[1]])
> ##D 	smc <- readSmc("fileName-0.txt")
> ## End(Not run)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>