Fit weighted and unweighted Cauchy and Normal distributions

Description

Functions to fit the probability density functions on ratio distribution.

Usage

fitCauchy(x)
fitNorm(x, portion = 0.75)
fitWeightedNorm(x, weights)
fitNormalCauchyMixture(x)
fitGaussianMixture(x, n = 500)
fitTlsd(x)

Arguments

Value

Cauchy,Norm

Author(s)

Florian P Breitwieser, Jacques Colinge.

See Also

proteinRatios

Examples

library(distr)
data(ibspiked_set1)
data(noise.model.hcd)
# calculate protein ratios of Trypsin and CERU_HUMAN. Note: this is only
#  for illustration purposes. For estimation of sample variability, data
#  from all protein should be used
pr <- proteinRatios(ibspiked_set1,noise.model=noise.model.hcd,
                    cl=as.character(c(1,1,2,2)),combn.method="intraclass",protein=c("136429","P00450"))

# fit a Cauchy distribution
ratiodistr <- fitCauchy(pr$lratio)
plot(ratiodistr)

Results

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> library(isobar)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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Welcome to Bioconductor

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

Welcome to isobar (v 1.18.0)
   'openVignette("isobar")' and '?isobar' provide help on usage.


Attaching package: 'isobar'

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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/isobar/fit-distr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fit distributions
> ### Title: Fit weighted and unweighted Cauchy and Normal distributions
> ### Aliases: fitCauchy fitTlsd fitNorm fitWeightedNorm
> ###   fitNormalCauchyMixture fitGaussianMixture
> 
> ### ** Examples
> 
> library(distr)
Loading required package: startupmsg
:startupmsg>  Utilities for Start-Up Messages (version 0.9.3)
:startupmsg> 
:startupmsg>  For more information see ?"startupmsg",
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:SweaveListingUtils>  ?"SweaveListingoptions".
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:SweaveListingUtils>  For more information see
:SweaveListingUtils>  ?"SweaveListingUtils",
:SweaveListingUtils>  NEWS("SweaveListingUtils")
:SweaveListingUtils>  There is a vignette to this
:SweaveListingUtils>  package; try
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> data(ibspiked_set1)
> data(noise.model.hcd)
> # calculate protein ratios of Trypsin and CERU_HUMAN. Note: this is only
> #  for illustration purposes. For estimation of sample variability, data
> #  from all protein should be used
> pr <- proteinRatios(ibspiked_set1,noise.model=noise.model.hcd,
+                     cl=as.character(c(1,1,2,2)),combn.method="intraclass",protein=c("136429","P00450"))
ratios 115 vs 114
ratios 117 vs 116
> 
> # fit a Cauchy distribution
> ratiodistr <- fitCauchy(pr$lratio)
> plot(ratiodistr)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>