| makeExprSet {celsius} | R Documentation |
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.
makeExprSet( celsiusObject, id = NULL, cvterm = NULL, feature = NULL, annotations = FALSE, mapids = FALSE)
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 |
Return value is a BIOC expression set object.
Marc Carlson and Allen Day
#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 );