converts cellHTS objects to dataframes

Description

converts a cellHTS2 object into a data.frame object and check that all mandatory meta data is included. Adds Directions, replicates and Pair columns.

Usage

cellHTS2df(x,neutral)

Arguments

Value

data.frame, with the data from the cellHTS object in column "value". Meta data from annotation file and the new columns; Directions, Replicate and Pair

Author(s)

Elin Axelsson

See Also

cellHTS

Examples

data(screen1_raw)
df = cellHTS2df(screen1_raw,neutral="Fluc")
head(df)

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)

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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(coRNAi)
Loading required package: cellHTS2
Loading required package: RColorBrewer
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/coRNAi/cellHTS2df.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cellHTS2df
> ### Title: converts cellHTS objects to dataframes
> ### Aliases: cellHTS2df
> 
> ### ** Examples
> 
> data(screen1_raw)
> df = cellHTS2df(screen1_raw,neutral="Fluc")
> head(df)
    plate well controlStatus ID1     ID2      GeneID        Pair Direction
1.1     1  A01        sample fwd     pbl     fwd pbl     pbl fwd         2
1.2     1  A02        sample fwd CG16935 fwd CG16935 fwd CG16935         1
1.3     1  A03        sample fwd  CG3165  fwd CG3165  fwd CG3165         1
1.4     1  A04        sample fwd    CSN4    fwd CSN4    fwd CSN4         1
1.5     1  A05        sample fwd    Rho1    fwd Rho1    fwd Rho1         1
1.6     1  A06        sample fwd    Fluc    fwd Fluc    fwd Fluc         1
         Type     value replicate
1.1      comb 257085712         1
1.2      comb 183081072         1
1.3      comb 204826160         1
1.4      comb 135301968         1
1.5      comb 309041728         1
1.6 controlN1 221808976         1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>