unable to find an inherited method for function 'rowData' for signature '“logical”'
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
asked Nov 24 '18 at 9:29
AngeloAngelo
1,60462345
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.
r knitr
asked Nov 24 '18 at 9:29
AngeloAngelo
1,60462345
You are placing the$usein the wrong place, I believe it should berowData(sce_list[[i]]$use), it is a member of the list, not from the function's return value.
– Rui Barradas
Nov 25 '18 at 21:26
2
usecat()to print out the value ofias you go along, you can see where the error occurs. Then inspect the relevant element ofsce_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]]$use)] Now I have a new error message Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'rowData' for signature '"logical"' Calls: <Anonymous> ... withVisible -> eval -> eval -> [ -> rowData -> <Anonymous> Execution halted
– Angelo
Nov 25 '18 at 22:57
What package containsrowData?
– user2554330
Nov 27 '18 at 0:27
Hi, The package scater used for single cell experiment data analysis.
– Angelo
Nov 27 '18 at 8:45
add a comment |
I have an R markdown code chunk that looks like this ( it is a small part of an extremely large code).
filterLowExpressedGenes <- function(sce, cutoffCell, cutoffTranscript){
apply(
counts(sce[ , colData(sce)$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]]$use)]
}
```
The error that I get is:
Quitting from lines 331-345 (prototype.Rmd)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'rowData' for signature '"logical"'
Calls: <Anonymous> ... withVisible -> eval -> eval -> [ -> rowData -> <Anonymous>
Execution halted
I am sorry, I cannot provide you the sample workable data. As this is somewhat in between coding portion and that means that data has already gone under some sort of processing.
I am fully aware that it will require some guess work or hit and trial to figure out the solution. But any help/suggestion to make this work is welcome.
Thank you in advance.
r knitr
asked Nov 24 '18 at 9:29
AngeloAngelo
1,60462345
I have an R markdown code chunk that looks like this ( it is a small part of an extremely large code).
filterLowExpressedGenes <- function(sce, cutoffCell, cutoffTranscript){
apply(
counts(sce[ , colData(sce)$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]]$use)]
}
```
The error that I get is:
Quitting from lines 331-345 (prototype.Rmd)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'rowData' for signature '"logical"'
Calls: <Anonymous> ... withVisible -> eval -> eval -> [ -> rowData -> <Anonymous>
Execution halted
I am sorry, I cannot provide you the sample workable data. As this is somewhat in between coding portion and that means that data has already gone under some sort of processing.
I am fully aware that it will require some guess work or hit and trial to figure out the solution. But any help/suggestion to make this work is welcome.
Thank you in advance.
r knitr
r knitr
asked Nov 24 '18 at 9:29
AngeloAngelo
1,60462345
asked Nov 24 '18 at 9:29
AngeloAngelo
1,60462345
edited Nov 26 '18 at 9:58
Angelo
asked Nov 24 '18 at 9:29
AngeloAngelo
1,60462345
asked Nov 24 '18 at 9:29
AngeloAngelo
1,60462345
asked Nov 24 '18 at 9:29
AngeloAngelo
1,60462345
1,60462345
You are placing the$usein the wrong place, I believe it should berowData(sce_list[[i]]$use), it is a member of the list, not from the function's return value.
– Rui Barradas
Nov 25 '18 at 21:26
2
usecat()to print out the value ofias you go along, you can see where the error occurs. Then inspect the relevant element ofsce_list...
– Ben Bolker
Nov 25 '18 at 22:29
@RuiBarradas: Hi, Thank you for your comment. I did move little forward. what I did was sce_list[[i]]$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 containsrowData?
– 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$usein the wrong place, I believe it should berowData(sce_list[[i]]$use), it is a member of the list, not from the function's return value.
– Rui Barradas
Nov 25 '18 at 21:26
2
usecat()to print out the value ofias you go along, you can see where the error occurs. Then inspect the relevant element ofsce_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 containsrowData?
– 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
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
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
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]]$use)] Now I have a new error message Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'rowData' for signature '"logical"' Calls: <Anonymous> ... withVisible -> eval -> eval -> [ -> rowData -> <Anonymous> Execution halted
– Angelo
Nov 25 '18 at 22:57
@RuiBarradas: Hi, Thank you for your comment. I did move little forward. what I did was sce_list[[i]]$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
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
Hi, The package scater used for single cell experiment data analysis.
– Angelo
Nov 27 '18 at 8:45
add a comment |
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You are placing the
$usein the wrong place, I believe it should berowData(sce_list[[i]]$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 ofias you go along, you can see where the error occurs. Then inspect the relevant element ofsce_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