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Last data update: 2014.03.03

R: make configurations for experimental design written in csv...

makeConf

R Documentation

make configurations for experimental design written in csv sheet

Description

Make a list with two elements. The first element is a data frame containing two group comparison study information. The second element is the design matrix.

Usage

	makeConf(sampleSheet)

Arguments

sampleSheet

A csv sheet represents ChIP experiments design. It contains 6 columns,sampleID,condition,factor,ipReads,ctReads,peaks. condition refers to treatment condition or cell line; factor refers to transcription factor or histone modification; ipReads is the ChIP sequence data in bam or bed format; ctReads is the control sequence data in bam or bed format; peaks is the called peaks from existing peak-calling software.

Value

A list with two elements. The first element is a data frame containing two group comparison study information. The second element is the design matrix.

Author(s)

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

Examples


	confs=makeConf(system.file("extdata", "conf.csv", package="ChIPComp"))
	conf=confs$conf
	design=confs$design

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/makeConf.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeConf
> ### Title: make configurations for experimental design written in csv sheet
> ### Aliases: makeConf
> 
> ### ** Examples
> 
> 
> 	confs=makeConf(system.file("extdata", "conf.csv", package="ChIPComp"))
> 	conf=confs$conf
> 	design=confs$design
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>