Print top ranked differential binding sites

Description

Print top differential binding sites ranked by posterior probability in a decreasing order.

Usage

	
	## S3 method for class 'ChIPComp'
print(x,topK=10,...)

Arguments

Value

Print differential binding sites ranked by posterior probability

Author(s)

Hao Wu<hao.wu@emory.edu>, Li Chen <li.chen@emory.edu>

Examples

	data(seqData)
	seqData=ChIPComp(seqData)
	print(seqData)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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(ChIPComp)
Loading required package: GenomicRanges
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPComp/print.Rd_%03d_medium.png", width=480, height=480)
> ### Name: print.ChIPComp
> ### Title: Print top ranked differential binding sites
> ### Aliases: print.ChIPComp
> 
> ### ** Examples
> 
> 	data(seqData)
> 	seqData=ChIPComp(seqData)
> 	print(seqData)
     chr     start       end ip_c0_r1 ip_c0_r2 ip_c1_r1 ip_c1_r2     ct_c0_r1
24 chr17  41462793  41468134     3626     4356       23        9 7.000000e+00
47 chr15  75309902  75327463      572      684      530      214 4.239901e+00
45  chr7 127281200 127558864      785     1030     4789     2459 9.204285e+00
8   chrX 153029492 153033027       44       36      746      336 2.666667e+00
2  chr19  16995963  17005821      283      280     1994     1054 6.076023e+00
53  chr9  34663975  34667049      418      531      235      173 2.666667e+00
14  chr1  36770095  36773714      194      250       18       11 4.000000e+00
28 chr14  55213729  55245520      249      237     2274      690 7.158971e+00
56  chr5 141389307 141389421        0        0        5        8 6.725728e-05
50  chr4 166244574 166254595      258      307      898      388 8.625731e+00
       ct_c0_r2     ct_c1_r1     ct_c1_r2 commonPeak prob.post  pvalue.wald
24 7.000000e+00 1.608187e+00 1.608187e+00          1 1.0000000 0.000000e+00
47 4.239901e+00 1.900000e+01 1.900000e+01          1 0.9999912 0.000000e+00
45 9.204285e+00 2.125000e+01 2.125000e+01          1 0.9999165 0.000000e+00
8  2.666667e+00 4.444444e+00 4.444444e+00          1 0.9928872 1.059262e-10
2  6.076023e+00 1.047368e+01 1.047368e+01          1 0.9912081 2.220446e-16
53 2.666667e+00 3.666667e+00 3.666667e+00          1 0.9857750 2.886580e-15
14 4.000000e+00 2.444444e+00 2.444444e+00          1 0.9772349 1.565828e-09
28 7.158971e+00 2.125000e+01 2.125000e+01          1 0.9600753 2.657446e-09
56 6.725728e-05 1.922092e-04 1.922092e-04          0 0.9359081 1.284754e-02
50 8.625731e+00 1.100000e+01 1.100000e+01          1 0.7351641 4.046903e-10
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>