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Last data update: 2014.03.03

R: Binomial test for REDseq dataset

binom.test.REDseq

R Documentation

Binomial test for REDseq dataset

Description

For any early stage experiment with one experimental condition and one biological replicate, binom.test.REDseq computes p-value for each RE site in the genome.

Usage

binom.test.REDseq(REsummary, col.count = 2, multiAdj = TRUE, 
multiAdjMethod = "BH", prior.p = 0.000001)

Arguments

`REsummary`	A matrix returned from summarizeByRE with a RE id column, a count/weight column. See examples
`col.count`	The column where the total count/weight is
`multiAdj`	Whether apply multiple hypothesis testing adjustment, TURE or FALSE
`multiAdjMethod`	Multiple testing procedures, for details, see mt.rawp2adjp in multtest package
`prior.p`	It is the probability of assigning a mapped sequence tag to a given RE site. Assuming each RE site gets cut equally, then the prior.p = 1/number of total RE sites in the genome.

Value

`p.value`	p-value of the test
`*.count`	weight/count from the input REsummary
`REid`	the id of the restriction enzyme from the input REsummary
`cut.frequency`	cut frequency
`*.adjusted.p.value`	applicable if multiAdj=TRUE, adjusted p.value using * method specified in multiAdjMethod

Author(s)

Lihua Julie Zhu

Examples

	library(REDseq)
	REsummary = cbind(c("RE1", "RE2", "RE3"), c(10,1,100))
	colnames(REsummary) = c("REid", "control")
	binom.test.REDseq(REsummary)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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/binom.test.REDseq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: binom.test.REDseq
> ### Title: Binomial test for REDseq dataset
> ### Aliases: binom.test.REDseq
> ### Keywords: Statistics
> 
> ### ** Examples
> 
> 	library(REDseq)
> 	REsummary = cbind(c("RE1", "RE2", "RE3"), c(10,1,100))
> 	colnames(REsummary) = c("REid", "control")
> 	binom.test.REDseq(REsummary)
       p.value control.count REid cut.frequency BH.adjusted.p.value
1 0.000000e+00           100  RE3   0.900900901        0.000000e+00
2 5.153623e-47            10  RE1   0.090090090        7.730435e-47
3 1.109939e-04             1  RE2   0.009009009        1.109939e-04
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>