nFeatures: How many features in a group?

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

Description

This function computes the number of features in the group defined by the feature variable fcol and appends this information in the feature data of object.

Usage

nFeatures(object, fcol)

Arguments

object	An instance of class MSnSet.
fcol	Feature variable defining the feature grouping structure.

Value

An updated MSnSet with a new feature variable fcol.nFeatures.

Author(s)

Laurent Gatto

Examples

library(pRolocdata)
data("hyperLOPIT2015ms3r1psm")
hyperLOPIT2015ms3r1psm <- nFeatures(hyperLOPIT2015ms3r1psm,
                                    "Protein.Group.Accessions")
i <- c("Protein.Group.Accessions", "Protein.Group.Accessions.nFeatures")
fData(hyperLOPIT2015ms3r1psm)[1:10, i]

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


This is pRolocdata version 1.28.0.
Use 'pRolocdata()' to list available data sets.
    Protein.Group.Accessions Protein.Group.Accessions.nFeatures
136                   Q99PL5                                108
141                   P14901                                  7
169                   O89090                                  3
203                 O89032-3                                  1
238                   Q8R2M2                                 13
239                   Q9JIG7                                  3
261                   Q3TWI9                                  5
268                   Q8K0H5                                  2
274                   Q99NH0                                  9
276                   Q9CZD3                                 24

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