broad.pda.seq.clip.Pileup Class Reference

Collaboration diagram for broad.pda.seq.clip.Pileup:

Public Member Functions
	Pileup (String bamFile, String annotationBedFile, String subregionBedFile, String genomeFasta, Collection< Predicate< Alignment >> readFilters) throws IOException
	Pileup (String bamFile, String fragmentEndWig, String annotationBedFile, String subregionBedFile, String genomeFasta, String regionOverlapperCountFile, String peakRegionBedFile, Collection< Predicate< Alignment >> readFilters) throws IOException
Map< Annotation, Collection < EmpiricalDistribution > >	getShuffledPositionsAllRegions (boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)
Map< Annotation, Double >	getScanPvalFragmentEndsMaxPositionAllRegionsBam (boolean fullyContained, Map< String, Double > nucProbs, int numPermutations, boolean fivePrimeEnd)
Map< Integer, Double >	getScanPvalsFragmentEndPileupsWig (Annotation region, boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)
Map< Annotation, Map< Integer, Double > >	getScanPvalsFragmentEndPileupsAllRegionsWig (boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)
void	writeScanPvalsFragmentEndPileupsAllRegionsWig (String outTable, String outBed, double pvalCutoffForBed, boolean fullyContained, Map< String, Double > nucProbs, int numPermutations) throws IOException
double	getScanPvalFragmentEndsMaxPositionBam (Annotation region, boolean fullyContained, Map< String, Double > nucProbs, int numPermutations, boolean fivePrimeEnd)
Collection< EmpiricalDistribution >	getShuffledPositions (Annotation region, boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)
EmpiricalDistribution	getFragmentEndsFromBamFile (Annotation region, boolean fullyContained, boolean fivePrimeEnd)
Map< String, Collection< Gene > >	getAnnotation ()

Static Public Member Functions
static void	main (String[] args) throws IOException

Detailed Description

Author

prussell

Constructor & Destructor Documentation

broad.pda.seq.clip.Pileup.Pileup	(	String	bamFile,
		String	annotationBedFile,
		String	subregionBedFile,
		String	genomeFasta,
		Collection< Predicate< Alignment >>	readFilters
	)		throws IOException

Parameters

bamFile	Bam file of alignments
annotationBedFile	Bed transcriptome annotation
genomeFasta	Fasta file of genome
readFilters	Read filters to use

Exceptions

IOException

Here is the caller graph for this function:

broad.pda.seq.clip.Pileup.Pileup	(	String	bamFile,
		String	fragmentEndWig,
		String	annotationBedFile,
		String	subregionBedFile,
		String	genomeFasta,
		String	regionOverlapperCountFile,
		String	peakRegionBedFile,
		Collection< Predicate< Alignment >>	readFilters
	)		throws IOException

Parameters

bamFile	Bam file of alignments
annotationBedFile	Bed transcriptome annotation
genomeFasta	Fasta file of genome
regionOverlapperCountFile	File of overlapper counts for regions (can be incomplete)
peakRegionBedFile	Bed file of peak region (subregion of the parent gene enclosing all reads overlapping the region) corresponding to each region. Bed name is the same as region name.
readFilters	Read filters to use

Exceptions

IOException

Member Function Documentation

Map<String, Collection<Gene> > broad.pda.seq.clip.Pileup.getAnnotation

(

)

Get the transcriptome annotation

Returns

The annotation

EmpiricalDistribution broad.pda.seq.clip.Pileup.getFragmentEndsFromBamFile	(	Annotation	region,
		boolean	fullyContained,
		boolean	fivePrimeEnd
	)

Get an empirical distribution storing the fragment ends of all fragments overlapping the region Fragment ends are in transcript coordinates with respect to the parent transcript

Parameters

parent	Parent gene
region	Region within parent to get pileup over
fullyContained	Only include fragments that are fully contained in the subregion
fivePrimeEnd	Report the 5' end of fragments (if false, reports 3' end)

Returns

Distribution of fragment endpoints in transcript coordinates

Here is the caller graph for this function:

Map<Annotation, Double> broad.pda.seq.clip.Pileup.getScanPvalFragmentEndsMaxPositionAllRegionsBam	(	boolean	fullyContained,
		Map< String, Double >	nucProbs,
		int	numPermutations,
		boolean	fivePrimeEnd
	)

For each region, find the highest fragment end pileup from the bam file. Randomly permute the fragments in a biased way according to background nucleotide probabilities. Get a scan P value for the real highest pileup in the region.

Parameters

fullyContained	When computing number of fragments and peak region, include fully contained fragments only
nucProbs	Background nucleotide probabilities
numPermutations	Number of permutations per region
fivePrimeEnd	Use the 5' end of fragments (if false, use 3' end)

Returns

Map of region to P value

Here is the call graph for this function:

double broad.pda.seq.clip.Pileup.getScanPvalFragmentEndsMaxPositionBam	(	Annotation	region,
		boolean	fullyContained,
		Map< String, Double >	nucProbs,
		int	numPermutations,
		boolean	fivePrimeEnd
	)

Find the highest fragment end pileup in the region from the bam file. Randomly permute the fragments in a biased way according to background nucleotide probabilities. Get a scan P value for the real highest pileup in the region.

Parameters

region	The region
fullyContained	When computing number of fragments and peak region, include fully contained fragments only
nucProbs	Background nucleotide probabilities
numPermutations	Number of permutations per region
fivePrimeEnd	Use the 5' end of fragments (if false, use 3' end)

Returns

Map of region to P value

Here is the call graph for this function:

Here is the caller graph for this function:

Map<Annotation, Map<Integer, Double> > broad.pda.seq.clip.Pileup.getScanPvalsFragmentEndPileupsAllRegionsWig	(	boolean	fullyContained,
		Map< String, Double >	nucProbs,
		int	numPermutations
	)

Randomly permute the fragments in a biased way according to background nucleotide probabilities. For each region get a scan P value for pileup height of each position in the region as read from wig file.

Parameters

fullyContained	If computing peak regions from the bam file, include fully contained fragments only
nucProbs	Background nucleotide probabilities
numPermutations	Number of permutations per region

Returns

Map of region to scan P value for each position in region

Here is the call graph for this function:

Here is the caller graph for this function:

Map<Integer, Double> broad.pda.seq.clip.Pileup.getScanPvalsFragmentEndPileupsWig	(	Annotation	region,
		boolean	fullyContained,
		Map< String, Double >	nucProbs,
		int	numPermutations
	)

Randomly permute the fragments in a biased way according to background nucleotide probabilities. Get a scan P value for pileup height of each position in the region as read from wig file.

Parameters

region	The region
fullyContained	If computing peak region from the bam file, include fully contained fragments only
nucProbs	Background nucleotide probabilities
numPermutations	Number of permutations

Returns

Scan P value for each position in region

Here is the call graph for this function:

Here is the caller graph for this function:

Collection<EmpiricalDistribution> broad.pda.seq.clip.Pileup.getShuffledPositions	(	Annotation	region,
		boolean	fullyContained,
		Map< String, Double >	nucProbs,
		int	numPermutations
	)

Get shuffled sets of positions within the span covered by fragments overlapping the region Each set contains a number of positions equal to the number of fragments overlapping the region Random shuffled positions are biased by nucleotide

Parameters

region	Region within parent gene
fullyContained	When getting the span covered by fragments overlapping the region, include fully contained fragments only
nucProbs	Background probabilities of each nucleotide; must add up to 1
numPermutations	Number of random sets to get

Returns

Collection of random position sets; each set is presented in an empirical distribution

Here is the caller graph for this function:

Map<Annotation, Collection<EmpiricalDistribution> > broad.pda.seq.clip.Pileup.getShuffledPositionsAllRegions	(	boolean	fullyContained,
		Map< String, Double >	nucProbs,
		int	numPermutations
	)

For each region get several shufflings of the positions

Parameters

fullyContained	When computing number of fragments and peak region, include fully contained fragments only
nucProbs	Background nucleotide probabilities
numPermutations	Number of permutations per region

Returns

Map of region to collection of random permutations

Here is the call graph for this function:

static void broad.pda.seq.clip.Pileup.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

Here is the call graph for this function:

void broad.pda.seq.clip.Pileup.writeScanPvalsFragmentEndPileupsAllRegionsWig	(	String	outTable,
		String	outBed,
		double	pvalCutoffForBed,
		boolean	fullyContained,
		Map< String, Double >	nucProbs,
		int	numPermutations
	)		throws IOException

Randomly permute the fragments in a biased way according to background nucleotide probabilities. For each region get a scan P value for pileup height of each position in the region as read from wig file. Write information to a table.

Parameters

outTable	Output table file
outBed	Bed file for significant positions
pvalCutoffForBed	P value cutoff for significant position
fullyContained	If computing peak regions from the bam file, include fully contained fragments only
nucProbs	Background nucleotide probabilities
numPermutations	Number of permutations per region

Returns

Map of region to scan P value for each position in region

Here is the call graph for this function:

---

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

• java/broad/pda/seq/clip/Pileup.java