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affysnpannotread

Read Affymetrix Mapping DNA array data from CSV-format annotation file

Syntax

AnnotStruct = affysnpannotread(File, PID)
AnnotStruct = affysnpannotread(File, PID, 'LookUpField', LookUpFieldValue)

Input Arguments

File

String specifying a file name or a path and file name of an Affymetrix® CSV annotation file for a Mapping 10K array set, Mapping 100K array set, or Mapping 500K array set.

If you specify only a file name, that file must be on the MATLAB® search path or in the current folder.

PID

String or cell array of strings specifying one or more probe set IDs on an Affymetrix mapping array.

LookUpFieldValueString or cell array of strings specifying one or more column headers in an Affymetrix CSV annotation file. Default are the fields shown in the following table.

Output Arguments

AnnotStruct

MATLAB structure containing information for one or more probe sets from File, an Affymetrix CSV annotation file.

AnnotStruct contains a subset of the fields in File. The fields are described in the table below.

Description

AnnotStruct = affysnpannotread(File, PID) reads File, an Affymetrix CSV annotation file for a Mapping 10K array set, Mapping 100K array set, or Mapping 500K array set, and returns AnnotStruct, a MATLAB structure containing annotation information for one or more probe sets specified by PID, a string or cell array of strings specifying one or more probe set IDs. AnnotStruct contains a subset of the fields in File. The fields are described in the following table.

Structure Created from an Affymetrix CSV Annotation File

FieldDescription
ProbeSetIDs

Cell array containing the unique probe set IDs specified by the PID input.

Chromosome

Cell array containing the chromosome number on which each probe set is located.

ChromPosition

Cell array containing the SNP genomic position on the chromosome for each probe set.

Cytoband

Cell array containing the cytogenetic banding region of the chromosome on which each probe set is located.

Sequence

Cell array containing the sequence of each probe set.

AlleleA

Cell array containing the base that is allele A for each probe set.

AlleleB

Cell array containing the base that is allele B for each probe set.

Accession

Cell array containing the GenBank® accession number for each probe set.

FragmentLength

Cell array containing the length of each probe set.

AnnotStruct = affysnpannotread(File, PID, 'LookUpField', LookUpFieldValue) returns annotation information from only the field (column) specified by LookUpFieldValue, a string or cell array of strings specifying one or more column headers in an Affymetrix CSV annotation file. Default are the fields shown in the previous table.

Examples

The following example assumes that you have the Mapping50K_Xba240.CDF file stored at C:\AffyLibFiles\, and that your current folder points to a location containing the Mapping50K_Xba240.na25.annot.csv annotation file.

  1. Use the affyread function to create a structure containing information from the Mapping50K_Xba240.CDF library file.

    cdf = affyread('C:\AffyLibFiles\Mapping50K_Xba240.CDF');
    
  2. Create a variable containing a cell array of the names of the probe sets, which are stored in the Name field of the ProbeSets field of the cdf structure.

    probesetIDs = {cdf.ProbeSets.Name}';
    
  3. Return a structure containing annotation information for all the probe sets in the Mapping50K_Xba240.na25.annot.csv annotation file.

    snpInfo = affysnpannotread('Mapping50K_Xba240.na25.annot.csv',probesetIDs)
    
    snpInfo = 
    
           ProbeSetIDs: {59024x1 cell}
            Chromosome: [59024x1 int8]
         ChromPosition: [59024x1 double]
              Cytoband: {59024x1 cell}
              Sequence: {59024x1 cell}
               AlleleA: {59024x1 cell}
               AlleleB: {59024x1 cell}
             Accession: {59024x1 cell}
        FragmentLength: [59024x1 double]
    

See Also

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