R: Perform hypothesis testing to detect differential binding...
ChIPComp
R Documentation
Perform hypothesis testing to detect differential binding sites
Description
Perform hypothesis testing to detect differential binding sites
Usage
ChIPComp(countSet,A,threshold=1)
Arguments
countSet
A ChIPComp object.
A
User-specified regions to fit the model.
It is a bed file with three columns, named ("chr","start","end"),
could be separated by space or tab.
threshold
User specified posterior probability threshold. Default is 1.
Value
A object ChIPComp contains
Column chr,start,end are the binding site genomic coordinate;
Column ip_c(#condition)_r(#replicate) indicates ChIP counts in #replicate in #condition;
Column ct_c(#condition)_r(#replicate) indicates smoothing control counts in #replicate in #condition;
Column commonPeak 1s indicate common binding sites;
Column prob.post is the posterior probability for each binding site.
Column pvalue.wald is the pvalue of wald test for each binding site.
Author(s)
Hao Wu<hao.wu@emory.edu>, Li Chen <li.chen@emory.edu>
Examples
data(seqData)
seqData=ChIPComp(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/ChIPComp.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ChIPComp
> ### Title: Perform hypothesis testing to detect differential binding sites
> ### Aliases: ChIPComp
>
> ### ** Examples
>
>
> data(seqData)
> seqData=ChIPComp(seqData)
>
>
>
>
>
>
> dev.off()
null device
1
>