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


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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.