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Last data update: 2014.03.03

R: Parse curv1Filter output

curvPeaks

R Documentation

Parse curv1Filter output

Description

Parse the output of curv1Filter and find modes and midpoints of the high-density regions. This function is considered to be internal.

Usage


curvPeaks(x, dat, borderQuant = 0.01, n = 201, from, to, densities=NULL)

Arguments

`x`	A `multipleFilterResult` produced by a `curv1Filter` operation.
`dat`	The corresponding `flowFrame`.
`borderQuant`	A numeric in `[0,1]` giving the extreme quantiles for which high-density regions are ignored.
`n, from, to`	Arguments are passed on to `density`.
`densities`	The optional y values of the density estimate computed for the respective data.

Value

A list with items

`peaks`	x and y locations of the modes of the regions in the density estimates.
`regions`	the left and right margins of the regions.
`midpoints`	the mean of `regions`.
`regPoints`	x and y locations of the outline of the significant density regions.
`densFuns`	an approximation function of the density estimate

Author(s)

Florian Hahne

Examples


data(GvHD)
tmp <- filter(GvHD[[10]], curv1Filter("FSC-H"))
res <-  flowStats:::curvPeaks(tmp, exprs(GvHD[[10]])[, "FSC-H"])

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(flowStats)
Loading required package: flowCore
Loading required package: fda
Loading required package: splines
Loading required package: Matrix

Attaching package: 'Matrix'

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

    %&%


Attaching package: 'fda'

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

    matplot

Loading required package: mvoutlier
Loading required package: sgeostat
sROC 0.1-2 loaded
Loading required package: cluster
Loading required package: flowWorkspace
Loading required package: flowViz
Loading required package: lattice
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: gridExtra
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowStats/curvPeaks.Rd_%03d_medium.png", width=480, height=480)
> ### Name: curvPeaks
> ### Title: Parse curv1Filter output
> ### Aliases: curvPeaks
> 
> ### ** Examples
> 
> 
> data(GvHD)
> tmp <- filter(GvHD[[10]], curv1Filter("FSC-H"))
> res <-  flowStats:::curvPeaks(tmp, exprs(GvHD[[10]])[, "FSC-H"])
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>