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 );