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

Description

RIPSeeker infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation. In addition, a rule-based approach is provided as an additional function named rulebaseRIPSeek for user to obtain RPKM/FPKM (and fold-change) for the gene/transcripts expressions in RIP (and control) based on automatically retrieved online Ensembl annotation given single or paired-end alignments.

Details

The front-end main function ripSeek suffices for most applications. The function takes as the only required argument the path to alignment files (BAM/BED/SAM) and outputs predicted RIP regions. Optionally, user may indicate via 'cNAME' which file(s) in the first file argument list is/are control to enable empirical false discover rate (eFDR) computation. If the arguments 'biomaRt_dataset' and/or 'goAnno' are set, ripSeek will return the annotated RIP predictions and the enriched GO terms corresponding to the genomic context of the RIP predictions. User can also specify the thresholds for statistical significance scores via logOddCutoff, pvalCutoff, pvalAdjCutoff, eFDRCutoff.

Author(s)

Yue Li <yueli@cs.toronto.edu>

References

Li, Y., Zhao, D. Y., Greenblatt, J. F., & Zhang, Z. (2013). RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Research. doi:10.1093/nar/gkt142

Zhao, J., Ohsumi, T. K., Kung, J. T., Ogawa, Y., Grau, D. J., Sarma, K., Song, J. J., et al. (2010). Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq. Molecular Cell, 40(6), 939D953. doi:10.1016/j.molcel.2010.12.011

See Also

ripSeek, rulebaseRIPSeek

Examples

library(RIPSeeker)

ls("package:RIPSeeker")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RIPSeeker)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicAlignments
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RIPSeeker/RIPSeeker-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RIPSeeker-package
> ### Title: RIPSeeker: a statistical package for identifying
> ###   protein-associated transcripts from RIP-seq experiments
> ### Aliases: RIPSeeker-package RIPSeeker
> ### Keywords: package high-throughput sequencing analysis RIP-seq Hidden
> ###   Markov model
> 
> ### ** Examples
> 
> 
> library(RIPSeeker)
> 
> ls("package:RIPSeeker")
 [1] "addDummyProb"           "addPseudoAlignment"     "annotateRIP"           
 [4] "binCount"               "combineAlignGals"       "combineRIP"            
 [7] "computeLogOdd"          "computeRPKM"            "disambiguateMultihits" 
[10] "empiricalFDR"           "evalBinSize"            "exportGRanges"         
[13] "galp2gal"               "getAlignGal"            "logScoreWithControl"   
[16] "logScoreWithoutControl" "mainSeek"               "mainSeekSingleChrom"   
[19] "nbh"                    "nbh.GRanges"            "nbh.integer"           
[22] "nbh_chk"                "nbh_em"                 "nbh_gen"               
[25] "nbh_init"               "nbh_vit"                "nbm_chk"               
[28] "nbm_em"                 "plotCoverage"           "plotStrandedCoverage"  
[31] "randindx"               "ripSeek"                "rulebaseRIPSeek"       
[34] "scoreMergedBins"        "seekRIP"                "selectBinSize"         
[37] "statdis"                "viewRIP"               
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>