naplot: Overview of missing value

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description

Visualise missing values as a heatmap and barplots along the samples and features.

Usage

naplot(
  object,
  verbose = isMSnbaseVerbose(),
  reorderRows = TRUE,
  reorderColumns = TRUE,
  ...
)

Arguments

object	An object of class MSnSet.
verbose	If verbose (default is isMSnbaseVerbose()), print a table of missing values.
reorderRows	If reorderRows (default is TRUE) rows are ordered by number of NA.
reorderColumns	If reorderColumns (default is TRUE) columns are ordered by number of NA.
...	Additional parameters passed to image2.

Value

Used for its side effect. Invisibly returns NULL

Author(s)

Laurent Gatto

Examples

data(naset)
naplot(naset)

Example output

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

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: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

    smooth


This is MSnbase version 2.16.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:base’:

    trimws

MSnbase documentation built on Jan. 23, 2021, 2 a.m.