1. 发现报错

在进行monocle2发育轨迹的时候，从来么有报错的软件，竟然罢工了，出现了如下报错：

pData(HSMM_myo)$Total_mRNAs <- Matrix::colSums(exprs(HSMM_myo))

image.png

检查报错：

exprs(HSMM_myo)
Error in (function (classes, fdef, mtable)  : 
unable to find an inherited method for function ‘exprs’ for signature ‘"CellDataSet"’
HSMM_myo
CellDataSet (storageMode: environment)
assayData: 19055 features, 12856 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: AAACCTGAGAAGGACA-1.CM022-2-1
    AAACCTGAGACAAGCC-1.CM022-2-1 ... TTTGTCATCTGGCGTG-1.CM022-2-1
    (12856 total)
  varLabels: orig.ident nCount_RNA ... Size_Factor (96 total)
  varMetadata: labelDescription
featureData
  featureNames: Mrpl15 Lypla1 ... Gm14379 (19055 total)
  fvarLabels: gene_short_name
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  

这说明不是monocle2对象的问题，可能是函数的问题？

 exprs
standardGeneric for "exprs" defined from package "monocle3"

function (x) 
standardGeneric("exprs")
<bytecode: 0x51240ad0>
<environment: 0x5123d698>
Methods may be defined for arguments: x
Use  showMethods(exprs)  for currently available ones.

原来问题出在这里，exprs这里默认的是monocle3定义的函数，但monocle3与monocle2可能不一样，因此这里需要改一下，使用标准的函数，具体如下：

Biobase::exprs
standardGeneric for "exprs" defined from package "Biobase"

function (object) 
standardGeneric("exprs")
<bytecode: 0x6f5c7c0>
<environment: 0x6f61448>
Methods may be defined for arguments: object
Use  showMethods(exprs)  for currently available ones.
> str(exprs(HSMM_myo))
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘exprs’ for signature ‘"CellDataSet"’
> str(Biobase::exprs(HSMM_myo))
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  ..@ i       : int [1:17615233] 0 2 10 33 35 61 66 100 108 119 ...
  ..@ p       : int [1:12857] 0 1721 2404 3147 3683 7653 8219 8681 9273 9734 ...
  ..@ Dim     : int [1:2] 19055 12856
  ..@ Dimnames:List of 2
  .. ..$ : chr [1:19055] "Mrpl15" "Lypla1" "Tcea1" "Rgs20" ...
  .. ..$ : chr [1:12856] "AAACCTGAGAAGGACA-1.CM022-2-1" "AAACCTGAGACAAGCC-1.CM022-2-1" "AAACCTGAGACCTAGG-1.CM022-2-1" "AAACCTGAGAGAACAG-1.CM022-2-1" ...
  ..@ x       : num [1:17615233] 1 1 2 1 11 1 1 1 1 1 ...
  ..@ factors : list()

总结

最终命令改成了如下形式：

pData(HSMM_myo)$Total_mRNAs <- Matrix::colSums(Biobase::exprs(HSMM_myo))

虽然这个报错只是一个小问题，但是这个问题提示我们，不同的R包的版本不一样，可能函数也不一样，如果需要使用不同版本的同一个R包，可以考虑通过conda多构建几个环境。