makeExprSet {celsius}R Documentation

Retrieve data and or phenotype annotations from Celsius and package into a BIOC expression set object

Description

The following function retrieves a matrix of annotation data and also a matrix of expression data and then packages them into a BIOC expression object for the user. The function requires a list of annotation terms along with either a list of IDs OR a list of elements (or both). If a list of elements is also provided, then the function will return the slice of data that corresponds to the intersection of those elements on the IDs listed.

Usage

makeExprSet( celsiusObject, id = NULL, cvterm = NULL, feature = NULL,
  annotations = FALSE, mapids = FALSE)

Arguments

celsiusObject Provide a celsius server object with approriate URLs
id Provide a list of SN ID's
cvterm Provide a list of cvterms
feature Provide a vector of elements
annotations if TRUE, this includes supplementary annotations as terms
mapids if TRUE, this will map any foreign keys for the user and allow access to alternate data

Value

Return value is a BIOC expression set object.

Author(s)

Marc Carlson and Allen Day

Examples

#make a celsius instance
celsius = new( "celsiusServer",
  celsiusUrl = "http://celsius.genomics.ctrl.ucla.edu",
  platform = "HG-U133A" );

#get the data
exprSet = makeExprSet( celsius,
  id = c( "SN:1005595"),
  cvterm = c("MPATH:458") );

#get the data
exprSet = makeExprSet( celsius, id = c( "SN:1005595" ) );

#get the data
exprSet = makeExprSet( celsius, id = c( "SN:1005595" ),
  feature = c("201820_at", "202222_s_at") );

#change the transform option to TRUE
celsius@transform = TRUE;

#get data (with transform now = TRUE)
exprSet = makeExprSet( celsius,
  id = c( "SN:1005595", "SN:1000170" ),
  cvterm = c( "MA:0000415", "MPATH:458" ) );

#get the data (transform still = TRUE)
exprSet = makeExprSet( celsius,
  id = c( "SN:1005595", "SN:1000170" ),
  cvterm = c( "MA:0000415", "MPATH:458" ),
  feature = c( "201820_at", "202222_s_at" ) );

#change the transform option to FALSE
celsius@transform = FALSE;

#get the data (now with transform = FALSE)
exprSet = makeExprSet( celsius,
  cvterm = c( "MA:0000415", "MPATH:458" ),
  feature = c( "222152_at", "201820_at", "202222_s_at", "202508_s_at",
  "203296_s_at", "203400_s_at" ) );

#get the data
exprSet = makeExprSet( celsius, feature = c( "201820_at" ) );

#get the data
exprSet = makeExprSet( celsius,
  feature = c( "201820_at", "202222_s_at" ) );

#get the data
exprSet = makeExprSet( celsius,
  cvterm = c( "MA:0000415", "MPATH:458" ),
  feature = c( "201820_at", "202222_s_at" ) );

#get the data
exprSet = makeExprSet( celsius,
  cvterm = c( "MA:0000415" ),
  feature = c( "201820_at" ) );

#change the affy platform being sought
celsius@platform = "Mouse430_2";

#get the data (now for Mouse 430 2.0 arrays)
exprSet = makeExprSet( celsius,
  id = c( "GSE6210" ),
  cvterm = c( "MPATH:458", "MA:0000415" ),
  mapids = TRUE); 

#change the platform back to HG-U133A
celsius@platform = "HG-U133A";

#now get the data
#(mapids = TRUE, so now you can use foreign keys as sample ID's )
exprSet = makeExprSet( celsius,
  id = c( "26490", "26491", "26492" ),
  cvterm = c( "MPATH:458", "MA:0000415" ),
  feature = c( "201820_at", "202222_s_at", "202508_s_at", "203296_s_at",
  "203400_s_at" ),
  mapids = TRUE );

#get the data (annotations = TRUE, so you will get some extra data about
#each sample)
exprSet = makeExprSet( celsius,
  id = c( "SN:1005595", "SN:1000170" ),
  cvterm = c( "MA:0000415", "MPATH:458" ),
  feature = c( "201820_at", "202222_s_at" ),
  annotations = TRUE );


[Package celsius version 1.0.7 Index]