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 GappedAlignment 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 GappedAlignmentPairs to GappedAlignments |
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. |