aroma-project.org

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