Extract the transformation parameters from a flowTransResult

Description

Extracts the transformation parameters from a flowTransResult object

Usage

extractParams(x, dims = NULL)

Arguments

Value

A list of length length(dims). Each element contains a vector of parameters for transforming the particular dimension.The names of the list elements correspond to the names of the dimensions.

Note

flowTrans estimates common transformation parameters.

Author(s)

Greg Finak <greg.finak@ircm.qc.ca>, Raphael Gottardo <raphael.gottardo@ircm.qc.ca>

References

Finak G, Perez JM, Weng A, Gottardo R. Optimizing Data Transformation for Flow Cytometry. (Submitted)

See Also

summary, flowTrans, flowTransResult

Examples

m <- t(matrix(rnorm(10000),2))
colnames(m) <- c("A","B")
m <- flowFrame(m)
res <- flowTrans(m,"mclMultivBoxCox", c("A","B"), n2f=FALSE,
                 parameters.only=FALSE)
summary(res)
extractParams(res)

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 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(flowTrans)
Loading required package: flowCore
Loading required package: flowViz
Loading required package: lattice
Loading required package: flowClust
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:flowCore':

    normalize, sort

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: graph
Loading required package: RBGL
Loading required package: ellipse
Loading required package: mnormt
Loading required package: corpcor
Loading required package: clue

Attaching package: 'flowClust'

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

    box

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowTrans/extractParams.Rd_%03d_medium.png", width=480, height=480)
> ### Name: extractParams
> ### Title: Extract the transformation parameters from a flowTransResult
> ### Aliases: extractParams
> ### Keywords: manip
> 
> ### ** Examples
> 
> m <- t(matrix(rnorm(10000),2))
> colnames(m) <- c("A","B")
> m <- flowFrame(m)
> res <- flowTrans(m,"mclMultivBoxCox", c("A","B"), n2f=FALSE,
+                  parameters.only=FALSE)
> summary(res)
Transformation: 
[1] "mclMultivBoxCox"
Transformed Results: 
flowFrame object 'anonymous'
with 5000 cells and 2 observables:
  name desc    range  minRange maxRange
A    A    A 2.445571 -4.350703 2.445571
B    B    B 2.509381 -4.667896 2.509381
0 keywords are stored in the 'description' slot

Transformation parameters:
    theta 
0.9290501 
> extractParams(res)
$A
    theta 
0.9290501 

$B
    theta 
0.9290501 

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>