Auxilliary functions for experiments with microtitre plates

Description

Functions to manipulate indices or names of microtitre plates

Usage

alphaNames(row = 8, column = 12, order=c("column","row"))
repairAlphaName(x)
alphaNames2Pos(x)
rowcol2pos(row = 1, column=1, plateFormat=c("96","384"))

Arguments

Details

alphaNames returns so-called alpha well names in the form of [A-H][0-9][0-9] (i.e., A01, C03, D11, H12) for microtitre plates. The order of returned alphaNames is controlled by the option order, which can be set either as col or row

repairAlphaName attempts to fix incomplete alpha well names. Now it is mainly used to fix well names missing the leading 0 of numeric index, like A1.

alphaName2Pos returns the row and column number of the given alpha well name, in the form of two-column data frame with row and col as colnames.

rowcol2pos returns the row-wise position index of given row and column index.

Value

See details

Author(s)

Jitao David Zhang jitao_david.zhang@roche.com

Examples

wells <- alphaNames()

repairAlphaName("A1")

alphaNames2Pos(c("A01","B02","C03","H12"))

rowcol2pos(3,1)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(RTCA)
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: RColorBrewer
Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCA/alphaNames.Rd_%03d_medium.png", width=480, height=480)
> ### Name: alphaNames
> ### Title: Auxilliary functions for experiments with microtitre plates
> ### Aliases: alphaNames repairAlphaName alphaNames2Pos rowcol2pos
> 
> ### ** Examples
> 
> wells <- alphaNames()
> 
> repairAlphaName("A1")
[1] "A01"
> 
> alphaNames2Pos(c("A01","B02","C03","H12"))
    row column
A01   1      1
B02   2      2
C03   3      3
H12   8     12
> 
> rowcol2pos(3,1)
[1] 25
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>