unable to find an inherited method for function 'rowData' for signature '“logical”'

问题

I have an R markdown code chunk that looks like this ( it is a small part of an extremely large code).

  filterLowExpressedGenes <- function(sce, cutoffCell, cutoffTranscript){

            apply(
                counts(sce[ , colData(sce)$use]), 
                1, 
                function(x) length(x[x > cutoffTranscript]) >= cutoffCell)
       }
        ```


    ```{r include=T}
        for (i in seq_along(sce_list))
          {
         print(rowData(sce_list[[i]])$use <- filterLowExpressedGenes(sce_list[[i]], 3, 5))
        }

        ```

{r include=T} for (i in seq_along(sce_list)) { print(table(rowData(sce_list[[i]])$use)) }

Till here all works fine and the output is:

## [1] "sce_1"
## 
## FALSE  TRUE 
## 31852  1842 
## [1] "sce_2"
## 
## FALSE  TRUE 
## 31009  2685 
## [1] "sce_3"
## 
## FALSE  TRUE 
## 31560  2134 
## [1] "sce_4"
## 
## FALSE  TRUE 
## 31697  1997

The next chunk that operates on the information processed in the previous chunks throws up error:

code: 
    ```{r include=T}
     for (i in seq_along(sce_list))
       {
          sce_list[[i]]$qc = sce_list[[i]][rowData(sce_list[[i]]$use), colData(sce_list[[i]]$use)]
      }

    ```

The error that I get is:

    Quitting from lines 331-345 (prototype.Rmd) 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'rowData' for signature '"logical"'
Calls: <Anonymous> ... withVisible -> eval -> eval -> [ -> rowData -> <Anonymous>
Execution halted

I am sorry, I cannot provide you the sample workable data. As this is somewhat in between coding portion and that means that data has already gone under some sort of processing.

I am fully aware that it will require some guess work or hit and trial to figure out the solution. But any help/suggestion to make this work is welcome.

Thank you in advance.

来源：https://stackoverflow.com/questions/53456853/unable-to-find-an-inherited-method-for-function-rowdata-for-signature-logica

标签

knitr