broad.core.motif.PWMUtils Class Reference

Collaboration diagram for broad.core.motif.PWMUtils:

Static Public Member Functions
static void	main (String[] args) throws IllegalArgumentException, Exception
static double[]	computeSequenceBGSequences (Map< String, Sequence > chrsByName, AnnotationReader<?extends GenomicAnnotation > reader) throws IOException
static Map < PositionWeightMatrix, LightweightGenomicAnnotation >	scanRegion (int shuffles, String prefix, double minScoreToWrite, boolean maxOnly, String outdir, List< PositionWeightMatrix > pwms, String chr, Annotation annot, double[] bgNucleotideFreqs, short[] encChrSeq) throws IOException

Static Public Attributes
static final String	USAGE

Member Function Documentation

static double [] broad.core.motif.PWMUtils.computeSequenceBGSequences ( Map< String, Sequence >  chrsByName, AnnotationReader<?extends GenomicAnnotation >  reader  ) throws IOException

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static void broad.core.motif.PWMUtils.main ( String[]  args ) throws IllegalArgumentException, Exception

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static Map<PositionWeightMatrix, LightweightGenomicAnnotation > broad.core.motif.PWMUtils.scanRegion ( int  shuffles, String  prefix, double  minScoreToWrite, boolean  maxOnly, String  outdir, List< PositionWeightMatrix >  pwms, String  chr, Annotation  annot, double[]  bgNucleotideFreqs, short[]  encChrSeq  ) throws IOException

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Member Data Documentation

final String broad.core.motif.PWMUtils.USAGE

static

Initial value:

= "Usage: ArrayDesignUtilities TASK=<task_num> <task_args>\n" +
    "\tTasks:\n" +
    "\t\t1. Compute log likelohood score thresholds for a given PWM set. This task will compute the distribution of scores then output thresholds for commonly used quantiles. -pwm <File containing one or more PWM matrices> -pA <new equilibrium probability for A>  -pC <new equilibrium probability for C>  -pG <new equilibrium probability for G>  -pT <new equilibrium probability for T> -out <file name for score quantile cutoff per pwm file or standard out if none is specified> -outdir <output directory or current directory if this parameter is not specified> [-prefix <A prefix for each pwm distribution file>]> " +
    "\n\t\tscan. Scan a set a set of genomic regions for PWM ocurrencens -pwm <File containing one or more PWM matrices> -regions <Genomic Annotations> -seqdir <Sequence directory> -maxOnly <If only the maximal hit per region should be reported> -outdir <Output directory to write output file> [-minScoreToWrite <Filter output by minimum score, reudces output file size> -prefix <Prefix to use for each PWM hit file> -shuffles <Number of pwm shuffles to asses significance>]"+
    "\n\t\tpermute. Permute a PWM matrix -pwm <File contining one or more PWM matrics> -out <Output file with permuted matrices or standard out in not specified>"+
    "\n\t\treverse. Reverse-compliment a PWM -pwm <File contining one or more PWM matrics> -out <Output file with permuted matrices or standard out in not specified>" +
    "\n\t\tscanGenome. Scan the genome for PWM ocurrencens -pwm <File containing one or more PWM matrices> -seqdir <Sequence directory> -outdir <Output directory to write output file> -minScoreToWrite <Filter output by minimum score, reudces output file size> [-prefix <Prefix to use for each PWM hit file> -shuffles <Number of pwm shuffles to asses significance>]"+
    "\n"

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The documentation for this class was generated from the following file:

• java/broad/core/motif/PWMUtils.java