readGmt

Description

This function will read a "gmt" file into R, returning results as a list of SMC objects.

Usage

readGmt(fname)

Arguments

Details

The .gmt file format is a tab delimited file format used to store gene lists. These gene lists are stored row by row. The first column is the gene set name. The second column is a brief description, and every entry after that is a gene within that gene set.

Value

A list of SMC objects

Author(s)

Karl Dykema <karl.dykema@vai.org>

References

http://www.broad.mit.edu/gsea/doc/data_formats.html#gmt

See Also

writeGmt

Examples

	datadir <- system.file("extdata", package = "PGSEA")
	sample <- readGmt(file.path(datadir, "sample.gmt"))
	str(sample)

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(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/readGmt.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readGmt
> ### Title: readGmt
> ### Aliases: readGmt
> ### 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" ...
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>