affysnpintensitysplit - Split Affymetrix SNP probe intensity information for alleles A and B

Syntax

Input Arguments

ProbeStruct	MATLAB structure containing probe intensity information from an Affymetrix Mapping DNA array, such as returned by celintensityread.
ControlsValue	Controls the inclusion of control probes in ProbeStructSplit. Choices are true or false (default).

Output Arguments

ProbeStructSplit

MATLAB structure containing probe intensity information from an Affymetrix Mapping DNA array, split into information for alleles A and B.

Description

ProbeStructSplit = affysnpintensitysplit(ProbeStruct) splits ProbeStruct, a structure containing probe intensity information from an Affymetrix Mapping DNA array, into ProbeStructSplit, a structure containing probe intensity information from an Affymetrix Mapping DNA array, split into information for alleles A and B.

ProbeStructSplit contains the following fields.

Field	Description
CDFName	File name of the Affymetrix CDF library file.
CELNames	Cell array of names of the Affymetrix CEL files.
NumChips	Number of CEL files read into the input structure.
NumProbeSets	Number of probe sets in each CEL file.
NumProbes	Maximum number of probes for just one allele in each CEL file. Note   If the number of probes for allele A is not the same as for allele B, the larger number is used.
ProbeSetIDs	Cell array of the probe set IDs from the Affymetrix CDF library file.
ProbeIndices	Column vector containing probe indexing information for just one allele in each cell file. Probes within a probe set are numbered 0 through N - 1, where N is the number of probes for one allele in the probe set. Note   ProbeIndices has the same number of elements as NumProbes.
PMAIntensities	Matrix containing perfect match (PM) probe intensity values for allele A. Each row corresponds to an allele A probe, and each column corresponds to a CEL file. The rows are ordered the same way as in ProbeIndices, and the columns are ordered the same way as in the CELFiles input argument to the celintensityread function.
PMBIntensities	Matrix containing perfect match (PM) probe intensity values for allele B. Each row corresponds to an allele B probe, and each column corresponds to a CEL file. The rows are ordered the same way as in ProbeIndices, and the columns are ordered the same way as in the CELFiles input argument to the celintensityread function.
MMAIntensities (optional)	Matrix containing mismatch (MM) probe intensity values for allele A. Each row corresponds to an allele A probe, and each column corresponds to a CEL file. The rows are ordered the same way as in ProbeIndices, and the columns are ordered the same way as in the CELFiles input argument to the celintensityread function.
MMBIntensities (optional)	Matrix containing mismatch (MM) probe intensity values for allele B. Each row corresponds to an allele B probe, and each column corresponds to a CEL file. The rows are ordered the same way as in ProbeIndices, and the columns are ordered the same way as in the CELFiles input argument to the celintensityread function.

ProbeStructSplit = affysnpintensitysplit(ProbeStruct, 'Controls', ControlsValue) controls the return of control probe intensities. Choices are true or false (default).

Note   Control probes sometimes contain information for only one allele. In this case, the value for the corresponding allele (A or B) that is not present is set to NaN.

Examples

The following example assumes that your current folder points to a location containing the Mapping50K_Hind240.CDF library file and 18 CEL files associated with this CDF library file. These files are associated with an Affymetrix Mapping DNA array.

1. Use the celintensityread function to read the Mapping50K_Hind240.CDF library file and 18 CEL files associated with it into a MATLAB structure.

   ps = celintensityread('*','Mapping50K_Hind240.CDF')
   
   ps = 
   
             CDFName: 'Mapping50K_Hind240.CDF'
            CELNames: {18x1 cell}
            NumChips: 18
        NumProbeSets: 57299
           NumProbes: 1145780
         ProbeSetIDs: {57299x1 cell}
        ProbeIndices: [1145780x1 uint8]
        GroupNumbers: [1145780x1 uint8]
       PMIntensities: [1145780x18 single]

2. Extract the PM probe intensities for allele A and allele B into another MATLAB structure, without including intensity information for the control probes.

   ps_split = affysnpintensitysplit(ps)
   
   ps_split = 
   
              CDFName: 'Mapping50K_Hind240.CDF'
             CELNames: {18x1 cell}
             NumChips: 18
         NumProbeSets: 57275
            NumProbes: 572750
          ProbeSetIDs: {57275x1 cell}
         ProbeIndices: [572750x1 uint8]
       PMAIntensities: [572750x18 single]
       PMBIntensities: [572750x18 single]

See Also

affyread | affysnpannotread | celintensityread

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