SELEX (version 1.4.0)

selex.defineSample: Define annotation for an individual sample

Description

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.

Usage

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

Arguments

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

Value

Details

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.

See Also

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

Examples

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