How to: Extract probeset summaries (chip effects) as an 'oligo' SnpQSet or SnpCnvQSet object

SnpChipEffectSet as SnpQSet

Probe-summarized SNP data can be exported as a SnpQSet object (defined in the oligo package) by calling:

sfs <- extractSnpQSet(ces)

where ces is an SnpChipEffectSet. Note that this will load all data in to memory.

Example: Mapping50K_Hind240

ces <- getChipEffectSet(plm)
print(ces)

## SnpChipEffectSet:  
## Name: HapMap270  
## Tags: 100K,CEU,testSet,QN,HapMapRef,RMA,oligo,+-  
## Path:
## plmData/HapMap270,100K,CEU,testSet,QN,HapMapRef,RMA,oligo,+-/Mapping50K_Hind240  
## Platform: Affymetrix  
## Chip type: Mapping50K_Hind240,monocell  
## Number of arrays: 6  
## Names: NA06985, NA06991, ..., NA07019  
## Time period: 2009-10-17 00:31:37 -- 2009-10-17 00:31:38  
## Total file size: 14.08MB  
## RAM: 0.01MB  
## Parameters: (probeModel: chr "pm", mergeStrands: logi FALSE)

eSet <- extractSnpQSet(ces)
print(eSet)

## SnpQSet (storageMode: lockedEnvironment)  
## assayData: 57244 features, 6 samples  
##   element names: antisenseThetaA, antisenseThetaB, senseThetaA,
## senseThetaB  
## phenoData  
##   sampleNames: NA06985,Hind,B5,3005533.CEL, NA06991,Hind,B6,3005533.CEL,
## ..., NA07019,Hind,A12,4000092.CEL  (6 total)  
##   varLabels and varMetadata description: none  
## featureData  
##   featureNames: SNP_A-1641748, SNP_A-1641750, ..., SNP_A-1757800
## (57244 total)  
##   fvarLabels and fvarMetadata description: none  
## experimentData: use 'experimentData(object)'  
## Annotation: pd.mapping50k.hind240

SnpChipEffectSet as SnpCnvQSet

Probe-summarized SNP data can be exported as a SnpCnvQSet object (defined in the oligo package) by calling:

eSet <- extractSnpCnvQSet(ces)

where ces is an SnpChipEffectSet. Note that this will load all data in to memory.

Example: GenomeWide_SNP_6

ces <- getChipEffectSet(plm)
print(ces)

## CnChipEffectSet:  
## Name: HapMap270  
## Tags: 6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,1array,AVG  
## Path:
## plmData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,1array,AVG/GenomeWide_SNP_6  
## Platform: Affymetrix  
## Chip type: GenomeWideSNP_6,Full,monocell  
## Number of arrays: 1  
## Names: NA06985  
## Time period: 2009-08-31 12:37:17 -- 2009-08-31 12:37:17  
## Total file size: 26.95MB  
## RAM: 0.00MB  
## Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
## combineAlleles: logi FALSE)


eSet <- extractSnpCnvQSet(ces)
print(eSet)

## SnpCnvQSet (storageMode: lockedEnvironment)  
## assayData: 931946 features, 3 samples  
##   element names: thetaA, thetaB  
## phenoData  
##   sampleNames: NA06985.CEL, NA06991.CEL, NA06993.CEL  
##   varLabels and varMetadata description: none  
## featureData  
##   featureNames: SNP_A-1780270, SNP_A-1780271, ..., SNP_A-8717615
## (931946 total)  
##   fvarLabels and fvarMetadata description: none  
## experimentData: use 'experimentData(object)'  
## Annotation: pd.genomewidesnp.6