R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Compare two RED Sequencing Dataset

compareREDseq

R Documentation

Compare two RED Sequencing Dataset

Description

For early stage experiment without replicates, compareREDseq outputs differentially cut RE sites between two experimental conditions using Fisher's Exact Test.

Usage

compareREDseq(REsummary, col.count1 = 2, col.count2 = 3, multiAdj = TRUE,
 multiAdjMethod = "BH", maxP = 1, minCount = 1)

Arguments

`REsummary`	A matrix with a RE id column, 2 count/weight column, see examples
`col.count1`	The column where the total count/weight for the 1st experimental condition is
`col.count2`	The column where the total count/weight for the 2nd experimental condition is
`multiAdj`	Whether apply multiple hypothesis testing adjustment, TURE or FALSE
`multiAdjMethod`	Multiple testing procedures, for details, see mt.rawp2adjp in multtest package
`maxP`	The maximum p-value to be considered to be significant
`minCount`	For a RE site to be included, the tag count from at least one of the experimental condictions >= minimumCount

Value

`p.value`	the p-value of the test
`*.count`	weight/count from the input column col.count1 and col.count2
`*.total`	total weight/count from input column col.count1 and col.count2
`REid`	the id of the restriction enzyme from the input
`odds.ratio`	an estimate of the odds ratio for 2nd experimental condition vs. 1st experimental condition
`*.adjusted.p.value`	applicable if multiAdj=TRUE, adjusted p.value using the method * specified in multiAdjMethod

Author(s)

Lihua Julie Zhu

Examples

library(REDseq)
x= cbind(c("RE1", "RE2", "RE3", "RE4"), c(10,1,100, 0),c(5,5,50, 40))
colnames(x) = c("REid", "control", "treated")
compareREDseq(x)

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(REDseq)
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: BSgenome.Celegans.UCSC.ce2
Loading required package: BSgenome
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: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: multtest
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: ChIPpeakAnno
Loading required package: grid
Loading required package: VennDiagram
Loading required package: futile.logger

No methods found in "IRanges" for requests: %in%
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/REDseq/compareREDseq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compareREDseq
> ### Title: Compare two RED Sequencing Dataset
> ### Aliases: compareREDseq
> ### Keywords: Statistics
> 
> ### ** Examples
> 
> library(REDseq)
> x= cbind(c("RE1", "RE2", "RE3", "RE4"), c(10,1,100, 0),c(5,5,50, 40))
> colnames(x) = c("REid", "control", "treated")
> compareREDseq(x)
       p.value control.count treated.count REid control.total treated.total
1 6.233642e-16             0            40  RE4           111           100
2 1.159388e-10           100            50  RE3           111           100
3 1.035503e-01             1             5  RE2           111           100
4 2.943364e-01            10             5  RE1           111           100
  odds.ratio BH.adjusted.p.value
1        Inf        2.493457e-15
2  0.1112945        2.318777e-10
3  5.7478720        1.380671e-01
4  0.5331227        2.943364e-01
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>