Question

我正在尝试从SingleR包中获取函数CreateSinglerObject，使其按照此处的指南工作：http://comphealth.ucsf.edu/SingleR/SingleR_create.html

很遗憾，我收到错误消息“找不到”。以下是我的输入和输出。版本是R-3.6.1。

感谢您能给我任何帮助。谢谢！

I / O

> library(Seurat)
Warning message:
In readRDS(path) : error reading from connection
> library(SingleR)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

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

    windows

Loading required package: GenomeInfoDb
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: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum


Attaching package: ‘SummarizedExperiment’

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

    Assays

> singler = CreateSinglerObject(ln, annot = NULL, min.genes = 0, technology = "10X", species = "Mouse", normalize.gene.length = F, variable.genes = "de", fine.tune = F, do.signatures = F, clusters = NULL, do.main.types = T, reduce.file.size = T, numCores = SingleR.numCores)
Error in CreateSinglerObject(ln, annot = NULL, min.genes = 0, technology = "10X",  : 
  could not find function "CreateSinglerObject"

Answer 1

{1,2,3}不再包含在CreateSinglerObject软件包中。它可能已被删除或重命名。显然，reference中甚至没有提到它。

就像评论中建议的那样，我将检查updated vignette以获得指示。似乎已被SingleR取代了，但是我对程序包还不够熟悉，无法肯定地说出来。

找不到函数“ CreateSinglerObject”

1 个答案: