# Functions for analyzing SELEX-seq data

## Documentation for package ‘SELEX’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

SELEX-package | SELEX Package
Selex | SELEX Package
selex | SELEX Package
selex.affinities | Construct a K-mer affinity table
selex.config | Set SELEX system parameters
selex.counts | Construct or retrieve a K-mer count table
selex.countSummary | Summarize available K-mer count tables
selex.defineSample | Define annotation for an individual sample
selex.exampledata | Extract example data files
selex.fastqPSFM | Construct a diagnostic PSFM for a FASTQ file
selex.getAttributes | Display sample handle properties
selex.getRound0 | Obtain round zero sample handle
selex.getSeqfilter | Display sequence filter attributes
selex.infogain | Compute or retrieve information gain between rounds
selex.infogainSummary | Summarize available information gain values
selex.jvmStatus | Display current JVM memory usage
selex.kmax | Calculate kmax for a dataset
selex.kmerPSFM | Construct a PSFM from a K-mer table
selex.loadAnnotation | Load a sample annotation file
selex.mm | Build or retrieve a Markov model
selex.mmProb | Compute prior probability of sequence using Markov model
selex.mmSummary | Summarize Markov model properties
selex.revcomp | Create forward-reverse complement data pairs
selex.run | Run a standard SELEX analysis
selex.sample | Create a sample handle
selex.samplePSFM | Construct a diagnostic PSFM for a FASTQ file
selex.sampleSummary | Show samples visible to the current SELEX session
selex.saveAnnotation | Save sample annotations to file
selex.seqfilter | Create a sequence filter
selex.setwd | Set or change the working directory
selex.split | Randomly split a dataset
selex.summary | Display all count table, Markov model, and information gain summaries