Residual dispersion estimates

Description

Estimates the residual dispersion of each row of a spectral counts matrix as the ratio residual variance to mean of mean values by level, for each factor in facs. Different plots are drawn to help in the interpretation of the results.

Usage

disp.estimates(msnset, facs=NULL, do.plot=TRUE, etit=NULL, to.pdf=FALSE, wait=TRUE)

Arguments

Details

Estimates the residual dispersion of each protein in the spectral counts matrix, for each factor in facs, and returns the quantiles at c(0.25, 0.5, 0.75, 0.9, 0.95, 0.99, 1) of the distribution of dispersion values for each factor. If facs is NULL the factors are taken from pData(msnset). If do.plot is TRUE this function produces a density plot of dispersion values, and the scatterplot of residual variance vs mean values, in log10 scale. If do.pdf is TRUE etit provides the root name for the pdf file name, ending with "-DispPlots.pdf". If etit is NULL a default value of "MSMS" is provided. A different set of plots is produced for each factor in facs.

Value

Invisibly returns a matrix with the quantiles at c(0.25, 0.5, 0.75, 0.9, 0.95, 0.99, 1) of the residual dispersion estimates. Each row has the residual dispersion values attribuable to each factor in facs.

Author(s)

Josep Gregori

Examples

data(msms.dataset)
msnset <- pp.msms.data(msms.dataset)
disp.q <- disp.estimates(msnset)
disp.q

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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> library(msmsEDA)
Loading required package: MSnbase
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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/msmsEDA/disp.estimates.Rd_%03d_medium.png", width=480, height=480)
> ### Name: disp.estimates
> ### Title: Residual dispersion estimates
> ### Aliases: disp.estimates
> ### Keywords: hplot distribution
> 
> ### ** Examples
> 
> data(msms.dataset)
> msnset <- pp.msms.data(msms.dataset)
> disp.q <- disp.estimates(msnset)
> disp.q
           0.25       0.5      0.75      0.9     0.95      0.99         1
treat 0.4470685 0.7500000 1.1111111 1.677193 2.474074 12.974250 67.206452
batch 0.2619048 0.4264069 0.6889895 1.279430 2.070838  5.640284  8.273493
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>