selex.defineSample: Define annotation for an individual sample
In SELEX: Functions for analyzing SELEX-seq data

Description Usage Arguments Details Value See Also Examples

A function used to manually load SELEX sample metadata and make it visible to the current session, which can then be used to create a sample handle (see selex.sample. It is functionally identical to selex.loadAnnotation, except constrained to take manual inputs for a single sample.

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selex.defineSample(seqName, seqFile=NULL, sampleName, round, varLength, 
  leftBarcode, rightBarcode, leftFlank=NULL, rightFlank=NULL, 
  round0SeqName=NULL, round0SampleName=NULL)

`seqName`	Desired sequencing run name
`seqFile`	Path to the FASTQ file containing the sample. Can be `NULL` if `seqFile` has been previously specified for the `seqName`.
`sampleName`	Desired sample name
`round`	Sample round
`varLength`	Length of the variable region
`leftBarcode`	Left barcode sequence
`rightBarcode`	Right barcode sequence
`leftFlank`	Left flank sequence
`rightFlank`	Right flank sequence
`round0SeqName`	The sequencing run name of the round 0 data associated with this sample
`round0SampleName`	The sample name of the round 0 data associated with this sample

selex.defineSample should be used for rapid testing or when it is not worthwhile to generate a generate a sample annotation file. Unlike selex.loadAnnotation, the unique name requirement is relaxed, requiring only unique seqName, seqFile, and round combinations. Only one seqFile can be specified for a given seqName; for example, the following will throw an error:

selex.defineSample('Seq1', 'Seq1.fastq.gz', round=1, rightBarcode='CCAGCTG', ...)
selex.defineSample('Seq1', 'Seq2.fastq.gz', round=2, rightBarcode='CCAGCTG', ...)

However, seqFile can be omitted if a new sample is being specified with the same seqName:

selex.defineSample('Seq1', 'Seq1.fastq.gz', round=1, rightBarcode='CCAGCTG', ...)
selex.defineSample('Seq1', NULL, round=1, rightBarcode='CCACGTC', ...)

The sequencing run name and sample name of the round 0 file associated with a later-round sample can be provided to keep samples and their random pools in order.

Not applicable

selex.getAttributes, selex.loadAnnotation, selex.sample, selex.sampleSummary, selex.saveAnnotation

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selex.defineSample(seqName='R0.libraries', seqFile=exampleFiles[1],
                sampleName='R0.barcodeGC', round = 0, varLength = 16, 
                leftBarcode = 'TGG', rightBarcode= 'CCAGCTG')