RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Documentation for package ‘RIPSeeker’ version 1.16.0

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RIPSeeker-package	RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
addDummyProb	Create a dummy GRanges object as a placeholder in case nbh_em fails (Internal function)
addPseudoAlignment	Add a psuedoalignment as a placeholder for the chromosome (Internal function)
annotateRIP	Annotate RIP peaks with genomic information and perform GO enrichement
binCount	Count reads in nonoverlapping bins across a chromosome
combineAlignGals	Combine alignment files into a single GAlignments object
combineRIP	Combined predictions from (presumably) biological replicates.
computeLogOdd	Compute the log odd ratio of RIP over background.
computeRPKM	Compute RPKM based on gene annotations
disambiguateMultihits	Assign each multihit to a unique region based on the posterior for the read-enriched hidden state
empiricalFDR	Compute empirical false discovery rate
evalBinSize	Evaluate bin size using Shimazaki cost function
exportGRanges	Export GRanges object in a specified format
galp2gal	Convert GAlignmentPairs to GAlignments
getAlignGal	Import and processs in BAM/SAM/BED format
logScoreWithControl	Compute RIPScore based on RIP and control posteriors and test for significance
logScoreWithoutControl	Compute RIPScore based on RIP posteriors alone and test for significance
mainSeek	Train HMM paramters on each chromosome independently from the alignments.
mainSeekSingleChrom	Automatic bin size selection, bin count, and HMM parameters optimization on read count vector from a single chromosome (Internal function)
nbh	Generic function of negative binomial HMM
nbh.GRanges	Optimize HMM parameters based on the read counts on a chromosome
nbh.integer	HMM posterior decoding and NB parameter optimization
nbh_chk	Check the parameters of the negative binomial HMM
nbh_em	Expectation conditional maximization of negative binomial HMM parameters using forward-backward algorithm
nbh_gen	Simulate data from a negative binomial HMM.
nbh_init	Initialize negative binomial HMM parameters using negative binomial mixture model
nbh_vit	Derive maximum likelihood hidden state sequence using Viterbi algorithm
nbm_chk	Check the parameters of the negative binomial mixture model
nbm_em	Expectation conditional maximization of likelihood for negative binomial mixture model
plotCoverage	Plot read coverage for a GRanges object
plotStrandedCoverage	Plot strand-specific read coverage for a GRanges object
randindx	Generates random indexes with a specified probability distribution
ripSeek	HMM-based de novo RIP predictions using alignment data
RIPSeeker	RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
rulebaseRIPSeek	Compute the RPKM and foldchange between two conditions for the annotated genes
scoreMergedBins	Average log odd scores over bins being merged into a single region
seekRIP	Identify significant peaks
selectBinSize	Select optimal bin size based on Shimazaki formula
statdis	Returns the stationary distribution of a Markov chain.
viewRIP	Visualize peaks from UCSC genome browser.