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

.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ height:90px;width:728px;box-sizing:border-box;
}

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.

edited Nov 26 '18 at 9:58

asked Nov 24 '18 at 9:29

Angelo

1,70462345

You are placing the $usein the wrong place, I believe it should be rowData(sce_list[[i]]$use), it is a member of the list, not from the function's return value.

– Rui Barradas
Nov 25 '18 at 21:26

2

use cat() to print out the value of i as you go along, you can see where the error occurs. Then inspect the relevant element of sce_list ...

– Ben Bolker
Nov 25 '18 at 22:29

@RuiBarradas: Hi, Thank you for your comment. I did move little forward. what I did was sce_list[[i]]$qc = sce_list[[i]][rowData(sce_list[[i]]$use), colData(sce_list[[i]]$use)] Now I have a new error message 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

– Angelo
Nov 25 '18 at 22:57

What package contains rowData?

– user2554330
Nov 27 '18 at 0:27

Hi, The package scater used for single cell experiment data analysis.

– Angelo
Nov 27 '18 at 8:45

add a comment |

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.

edited Nov 26 '18 at 9:58

asked Nov 24 '18 at 9:29

Angelo

1,70462345

You are placing the $usein the wrong place, I believe it should be rowData(sce_list[[i]]$use), it is a member of the list, not from the function's return value.

– Rui Barradas
Nov 25 '18 at 21:26

2

use cat() to print out the value of i as you go along, you can see where the error occurs. Then inspect the relevant element of sce_list ...

– Ben Bolker
Nov 25 '18 at 22:29

@RuiBarradas: Hi, Thank you for your comment. I did move little forward. what I did was sce_list[[i]]$qc = sce_list[[i]][rowData(sce_list[[i]]$use), colData(sce_list[[i]]$use)] Now I have a new error message 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

– Angelo
Nov 25 '18 at 22:57

What package contains rowData?

– user2554330
Nov 27 '18 at 0:27

Hi, The package scater used for single cell experiment data analysis.

– Angelo
Nov 27 '18 at 8:45

add a comment |

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.

edited Nov 26 '18 at 9:58

asked Nov 24 '18 at 9:29

Angelo

1,70462345

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.

r knitr

edited Nov 26 '18 at 9:58

asked Nov 24 '18 at 9:29

Angelo

1,70462345

edited Nov 26 '18 at 9:58

asked Nov 24 '18 at 9:29

Angelo

1,70462345

edited Nov 26 '18 at 9:58

asked Nov 24 '18 at 9:29

Angelo

1,70462345

asked Nov 24 '18 at 9:29

Angelo

1,70462345

asked Nov 24 '18 at 9:29

Angelo

1,70462345

You are placing the $usein the wrong place, I believe it should be rowData(sce_list[[i]]$use), it is a member of the list, not from the function's return value.

– Rui Barradas
Nov 25 '18 at 21:26

2

use cat() to print out the value of i as you go along, you can see where the error occurs. Then inspect the relevant element of sce_list ...

– Ben Bolker
Nov 25 '18 at 22:29

@RuiBarradas: Hi, Thank you for your comment. I did move little forward. what I did was sce_list[[i]]$qc = sce_list[[i]][rowData(sce_list[[i]]$use), colData(sce_list[[i]]$use)] Now I have a new error message 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

– Angelo
Nov 25 '18 at 22:57

What package contains rowData?

– user2554330
Nov 27 '18 at 0:27

Hi, The package scater used for single cell experiment data analysis.

– Angelo
Nov 27 '18 at 8:45

add a comment |

You are placing the $usein the wrong place, I believe it should be rowData(sce_list[[i]]$use), it is a member of the list, not from the function's return value.

– Rui Barradas
Nov 25 '18 at 21:26

2

use cat() to print out the value of i as you go along, you can see where the error occurs. Then inspect the relevant element of sce_list ...

– Ben Bolker
Nov 25 '18 at 22:29

@RuiBarradas: Hi, Thank you for your comment. I did move little forward. what I did was sce_list[[i]]$qc = sce_list[[i]][rowData(sce_list[[i]]$use), colData(sce_list[[i]]$use)] Now I have a new error message 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

– Angelo
Nov 25 '18 at 22:57

What package contains rowData?

– user2554330
Nov 27 '18 at 0:27

Hi, The package scater used for single cell experiment data analysis.

– Angelo
Nov 27 '18 at 8:45

You are placing the $usein the wrong place, I believe it should be rowData(sce_list[[i]]$use), it is a member of the list, not from the function's return value.

– Rui Barradas
Nov 25 '18 at 21:26

use cat() to print out the value of i as you go along, you can see where the error occurs. Then inspect the relevant element of sce_list ...

– Ben Bolker
Nov 25 '18 at 22:29

@RuiBarradas: Hi, Thank you for your comment. I did move little forward. what I did was sce_list[[i]]$qc = sce_list[[i]][rowData(sce_list[[i]]$use), colData(sce_list[[i]]$use)] Now I have a new error message 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

– Angelo
Nov 25 '18 at 22:57

What package contains rowData?

– user2554330
Nov 27 '18 at 0:27

Hi, The package scater used for single cell experiment data analysis.

– Angelo
Nov 27 '18 at 8:45

add a comment |

0

active

oldest

votes

Your Answer

StackExchange.ifUsing("editor", function () {
StackExchange.using("externalEditor", function () {
StackExchange.using("snippets", function () {
StackExchange.snippets.init();
});
});
}, "code-snippets");

StackExchange.ready(function() {
var channelOptions = {
tags: "".split(" "),
id: "1"
};
initTagRenderer("".split(" "), "".split(" "), channelOptions);

StackExchange.using("externalEditor", function() {
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled) {
StackExchange.using("snippets", function() {
createEditor();
});
}
else {
createEditor();
}
});

function createEditor() {
StackExchange.prepareEditor({
heartbeatType: 'answer',
autoActivateHeartbeat: false,
convertImagesToLinks: true,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: 10,
bindNavPrevention: true,
postfix: "",
imageUploader: {
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
},
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
});

}
});

draft saved

draft discarded

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53456853%2funable-to-find-an-inherited-method-for-function-rowdata-for-signature-logica%23new-answer', 'question_page');
}
);

Post as a guest

Name

Required, but never shown

0

active

oldest

votes

0

active

oldest

votes

draft saved

draft discarded

Thanks for contributing an answer to Stack Overflow!

Please be sure to answer the question. Provide details and share your research!

But avoid …

Asking for help, clarification, or responding to other answers.

Making statements based on opinion; back them up with references or personal experience.

To learn more, see our tips on writing great answers.

draft saved

draft discarded

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Name

Required, but never shown

Name

Required, but never shown

This page is only for reference, If you need detailed information, please check here

搜尋此網誌

Wsrtjtyk