defunct: Defunct functions

In scran: Methods for Single-Cell RNA-Seq Data Analysis

Description

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

Usage

trendVar(...)

decomposeVar(...)

testVar(...)

improvedCV2(...)

technicalCV2(...)

makeTechTrend(...)

multiBlockVar(...)

multiBlockNorm(...)

overlapExprs(...)

parallelPCA(...)

Arguments

...	Ignored arguments.

Details

trendVar, decomposeVar and testVar are succeeded by a suite of funtions related to modelGeneVar and fitTrendVar.

improvedCV2 and technicalCV2 are succeeded by modelGeneCV2 and fitTrendCV2.

makeTechTrend is succeeded by modelGeneVarByPoisson.

multiBlockVar is succeeded by the block argument in many of the modelling functions, and multiBlockNorm is no longer necessary.

overlapExprs is succeeded by findMarkers with test.type="wilcox".

parallelPCA has been moved over to the PCAtools package.

Value

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

Author(s)

Aaron Lun

Examples

try(trendVar())

Example output

Loading required package: BiocParallel
Loading required package: scater
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 (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'trendVar' for signature '"missing"'

scran documentation built on April 17, 2021, 6:09 p.m.