Fits a bivariate normal distribution into a data set of
paired values and selects data points according to their standard
deviation from the fitted distribution.
Numeric vector containing x-value or n by 2 matrix containing x and
y values or object of class cytoFrame.
y
Numeric vector containing y-value (optional). The length of x
must be the same as that of y.
scalefac
Numeric vector giving factor of standard deviations
used for data selection (all points within scalefac standard
deviations are selected).
method
One of covMcd or cov.rob defining method
used for computation of covariance matrix.
noise
Numeric or logical index vector defining value pairs in x
that are not used for fitting of distributions. Can be used to deal with
noisy data.
gateName
Character giving the name of the gate object.
Details
Computes the densities of a bivariate normal distribution from
the covariance matrix of the paired data. Covariance matrices are
acquired either by function covMcd
(considerably faster) or by function cov.rob.
Value
A list containing items mu (midpoint of distribution),
S (covariance matrix), p (density values for each
data pair), sel (selection of data points), scalefac
(factor of standard deviations used for data selection), data
(x and y values of data points) and gate, an object of class
gate containing the selection.
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(prada)
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: grid
Loading required package: rrcov
Loading required package: robustbase
Attaching package: 'robustbase'
The following object is masked from 'package:Biobase':
rowMedians
Scalable Robust Estimators with High Breakdown Point (version 1.3-11)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/prada/fitNorm2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fitNorm2
> ### Title: Fit bivariate normal distribution.
> ### Aliases: fitNorm2
>
> ### ** Examples
>
> sampdat <- readFCS(system.file("extdata",
+ "fas-Bcl2-plate323-04-04.A01", package="prada"))
> nfit <- fitNorm2(exprs(sampdat[,1:2]), scalefac=2)
> plotNorm2(nfit, selection=TRUE, ellipse=TRUE)
>
>
>
>
>
> dev.off()
null device
1
>