defunct: Defunct functions

In scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

Description

Functions that have passed on to the function afterlife. Their successors are also listed.

Usage

calculateQCMetrics(...)

## S4 method for signature 'SingleCellExperiment'
normalize(object, ...)

centreSizeFactors(...)

Arguments

object, ...

Ignored arguments.

Details

calculateQCMetrics is succeeded by perCellQCMetrics and perFeatureQCMetrics.

normalize is succeeded by logNormCounts.

centreSizeFactors has no replacement - the SingleCellExperiment is removing support for multiple size factors, so this function is now trivial.

Value

All functions error out with a defunct message pointing towards its descendent (if available).

Author(s)

Aaron Lun

Examples

try(calculateQCMetrics())

Example output

Loading required package: Biobase
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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

Loading required package: ggplot2

Attaching package: 'scater'

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

    filter

Error in is(object, "SCESet") : 
  argument "object" is missing, with no default

scater documentation built on Feb. 28, 2021, 2:01 a.m.