Exploring missing data in 'MSnSet' instances

Description

These methods produce plots that illustrate missing data.

is.na returns the expression matrix of it MSnSet argument as a matrix of logicals referring whether the corresponding cells are NA or not. It is generally used in conjunction with table and image (see example below).

The plotNA method produces plots that illustrate missing data. The completeness of the full dataset or a set of proteins (ordered by increasing NA content along the x axis) is represented. The methods make use the ggplot2 system. An object of class 'ggplot' is returned invisibly.

Methods

is.na

signature(x = "MSnSet")

Returns the a matrix of logicals of dimensions dim(x) specifiying if respective values are missing in the MSnSet's expression matrix.

plotNA

signature(object = "MSnSet", pNA = "numeric")

Plots missing data for an MSnSet instance. pNA is a numeric of length 1 that specifies the percentage of accepted missing data values per features. This value will be highlighted with a point on the figure, illustrating the overall percentage of NA values in the full data set and the number of proteins retained. Default is 1/2.

Author(s)

Laurent Gatto <lg390@cam.ac.uk>

See Also

See also the filterNA method to filter out features with a specified proportion if missing values.

Examples

data(msnset)
exprs(msnset)[sample(prod(dim(msnset)), 120)] <- NA

head(is.na(msnset))
table(is.na(msnset))
image(msnset)

plotNA(msnset, pNA = 1/4)

Results

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> library(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/MSnbase/plotNA-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotNA-methods
> ### Title: Exploring missing data in 'MSnSet' instances
> ### Aliases: plotNA-methods plotNA,MSnSet-method plotNA,matrix-method
> ###   plotNA is.na.MSnSet
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(msnset)
> exprs(msnset)[sample(prod(dim(msnset)), 120)] <- NA
> 
> head(is.na(msnset))
    iTRAQ4.114 iTRAQ4.115 iTRAQ4.116 iTRAQ4.117
X1       FALSE      FALSE      FALSE       TRUE
X10      FALSE       TRUE       TRUE      FALSE
X11      FALSE       TRUE       TRUE      FALSE
X12      FALSE       TRUE       TRUE       TRUE
X13      FALSE       TRUE      FALSE      FALSE
X14      FALSE       TRUE      FALSE       TRUE
> table(is.na(msnset))

FALSE  TRUE 
  100   120 
> image(msnset)
> 
> plotNA(msnset, pNA = 1/4)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>