Error in as.vector(x) : no method for coercing this S4 class to a vector
2
$begingroup$
I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error:
Error in as.vector(x) : no method for coercing this S4 class to a vector
My code:
library('dplyr')
library('recount')
library('magrittr')
library('ffpe')
library('RSkittleBrewer')
library('SummarizedExperiment')
library('devtools')
trop <- RSkittleBrewer::RSkittleBrewer('tropical')
colon_proj <- c('SRP025982', 'SRP42161')
if(any(!file.exists(file.path(colon_proj, 'rse_gene.Rdata')))) {
sapply(colon_proj, download_study)
}
blood_proj <- c('SRP066834', 'SRP041736', 'SRP060416')
if(any(!file.exists(file.path(blood_proj, 'rse_gene.Rdata')))) {
sapply(blood_proj, download_study)
}
proj <- c(colon_proj,blood_proj)
dat <- lapply(proj, function(x) {
load(file.path(x, 'rse_gene.Rdata'))
return(rse_gene)
})
proj
sapply(dat, dim)
metadata <- all_metadata('sra')
write.table(metadata, "recount_metadata.csv")
mdat <- do.call(cbind, dat)
write.table(mdat, "recount_mdat.csv")
is(mdat)
## "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" "Annotated"
rna-seq bioconductor rstudio
edited Feb 13 at 9:32
llrs
3,3261632
asked Feb 12 at 15:41
priyapriya
324
$endgroup$
add a comment |
2
$begingroup$
I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error:
Error in as.vector(x) : no method for coercing this S4 class to a vector
My code:
library('dplyr')
library('recount')
library('magrittr')
library('ffpe')
library('RSkittleBrewer')
library('SummarizedExperiment')
library('devtools')
trop <- RSkittleBrewer::RSkittleBrewer('tropical')
colon_proj <- c('SRP025982', 'SRP42161')
if(any(!file.exists(file.path(colon_proj, 'rse_gene.Rdata')))) {
sapply(colon_proj, download_study)
}
blood_proj <- c('SRP066834', 'SRP041736', 'SRP060416')
if(any(!file.exists(file.path(blood_proj, 'rse_gene.Rdata')))) {
sapply(blood_proj, download_study)
}
proj <- c(colon_proj,blood_proj)
dat <- lapply(proj, function(x) {
load(file.path(x, 'rse_gene.Rdata'))
return(rse_gene)
})
proj
sapply(dat, dim)
metadata <- all_metadata('sra')
write.table(metadata, "recount_metadata.csv")
mdat <- do.call(cbind, dat)
write.table(mdat, "recount_mdat.csv")
is(mdat)
## "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" "Annotated"
rna-seq bioconductor rstudio
edited Feb 13 at 9:32
llrs
3,3261632
asked Feb 12 at 15:41
priyapriya
324
$endgroup$
1
$begingroup$
What is the class of mdat? Did you tryis(mdat)? What did you get?
$endgroup$
– llrs
Feb 12 at 16:14
$begingroup$
@IIrs Hi I got this after this step [1] "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" [4] "Annotated"
$endgroup$
– priya
Feb 12 at 16:15
1
$begingroup$
Great, see how fast you got your answer when you provided enough details, remember to include all the relevant details next time! Glad you found how to solve the problem
$endgroup$
– llrs
Feb 13 at 9:31
add a comment |
2
2
2
$begingroup$
I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error:
Error in as.vector(x) : no method for coercing this S4 class to a vector
My code:
library('dplyr')
library('recount')
library('magrittr')
library('ffpe')
library('RSkittleBrewer')
library('SummarizedExperiment')
library('devtools')
trop <- RSkittleBrewer::RSkittleBrewer('tropical')
colon_proj <- c('SRP025982', 'SRP42161')
if(any(!file.exists(file.path(colon_proj, 'rse_gene.Rdata')))) {
sapply(colon_proj, download_study)
}
blood_proj <- c('SRP066834', 'SRP041736', 'SRP060416')
if(any(!file.exists(file.path(blood_proj, 'rse_gene.Rdata')))) {
sapply(blood_proj, download_study)
}
proj <- c(colon_proj,blood_proj)
dat <- lapply(proj, function(x) {
load(file.path(x, 'rse_gene.Rdata'))
return(rse_gene)
})
proj
sapply(dat, dim)
metadata <- all_metadata('sra')
write.table(metadata, "recount_metadata.csv")
mdat <- do.call(cbind, dat)
write.table(mdat, "recount_mdat.csv")
is(mdat)
## "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" "Annotated"
rna-seq bioconductor rstudio
edited Feb 13 at 9:32
llrs
3,3261632
asked Feb 12 at 15:41
priyapriya
324
$endgroup$
I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error:
Error in as.vector(x) : no method for coercing this S4 class to a vector
My code:
library('dplyr')
library('recount')
library('magrittr')
library('ffpe')
library('RSkittleBrewer')
library('SummarizedExperiment')
library('devtools')
trop <- RSkittleBrewer::RSkittleBrewer('tropical')
colon_proj <- c('SRP025982', 'SRP42161')
if(any(!file.exists(file.path(colon_proj, 'rse_gene.Rdata')))) {
sapply(colon_proj, download_study)
}
blood_proj <- c('SRP066834', 'SRP041736', 'SRP060416')
if(any(!file.exists(file.path(blood_proj, 'rse_gene.Rdata')))) {
sapply(blood_proj, download_study)
}
proj <- c(colon_proj,blood_proj)
dat <- lapply(proj, function(x) {
load(file.path(x, 'rse_gene.Rdata'))
return(rse_gene)
})
proj
sapply(dat, dim)
metadata <- all_metadata('sra')
write.table(metadata, "recount_metadata.csv")
mdat <- do.call(cbind, dat)
write.table(mdat, "recount_mdat.csv")
is(mdat)
## "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" "Annotated"
rna-seq bioconductor rstudio
rna-seq bioconductor rstudio
edited Feb 13 at 9:32
llrs
3,3261632
asked Feb 12 at 15:41
priyapriya
324
edited Feb 13 at 9:32
llrs
3,3261632
asked Feb 12 at 15:41
priyapriya
324
edited Feb 13 at 9:32
llrs
3,3261632
edited Feb 13 at 9:32
llrs
3,3261632
edited Feb 13 at 9:32
llrs
3,3261632
3,3261632
asked Feb 12 at 15:41
priyapriya
324
asked Feb 12 at 15:41
priyapriya
324
asked Feb 12 at 15:41
priyapriya
324
324
1
$begingroup$
What is the class of mdat? Did you tryis(mdat)? What did you get?
$endgroup$
– llrs
Feb 12 at 16:14
$begingroup$
@IIrs Hi I got this after this step [1] "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" [4] "Annotated"
$endgroup$
– priya
Feb 12 at 16:15
1
$begingroup$
Great, see how fast you got your answer when you provided enough details, remember to include all the relevant details next time! Glad you found how to solve the problem
$endgroup$
– llrs
Feb 13 at 9:31
add a comment |
1
$begingroup$
What is the class of mdat? Did you tryis(mdat)? What did you get?
$endgroup$
– llrs
Feb 12 at 16:14
$begingroup$
@IIrs Hi I got this after this step [1] "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" [4] "Annotated"
$endgroup$
– priya
Feb 12 at 16:15
1
$begingroup$
Great, see how fast you got your answer when you provided enough details, remember to include all the relevant details next time! Glad you found how to solve the problem
$endgroup$
– llrs
Feb 13 at 9:31
1
1
$begingroup$
What is the class of mdat? Did you try
is(mdat)? What did you get?$endgroup$
– llrs
Feb 12 at 16:14
$begingroup$
What is the class of mdat? Did you try
is(mdat)? What did you get?$endgroup$
– llrs
Feb 12 at 16:14
$begingroup$
@IIrs Hi I got this after this step [1] "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" [4] "Annotated"
$endgroup$
– priya
Feb 12 at 16:15
$begingroup$
@IIrs Hi I got this after this step [1] "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" [4] "Annotated"
$endgroup$
– priya
Feb 12 at 16:15
1
1
$begingroup$
Great, see how fast you got your answer when you provided enough details, remember to include all the relevant details next time! Glad you found how to solve the problem
$endgroup$
– llrs
Feb 13 at 9:31
$begingroup$
Great, see how fast you got your answer when you provided enough details, remember to include all the relevant details next time! Glad you found how to solve the problem
$endgroup$
– llrs
Feb 13 at 9:31
add a comment |
1 Answer
1
active
oldest
votes
4
$begingroup$
You can't cbind a bunch of obscure object types.
If you want merged count tables you should do this:
mdat <- do.call(cbind,lapply(dat,assay))
Where row.names are Ensembl gene IDs and col.names are the SRR accessions.
Then run your table writing command.
-
If you want the coordinates of your genes then do this to make a bed with the genomic locations:
library(rtracklayer)
export.bed(rowRanges(dat[[1]]),'gene_coords.bed')
answered Feb 12 at 17:10
storystory
758211
$endgroup$
add a comment |
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1 Answer
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active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
4
$begingroup$
You can't cbind a bunch of obscure object types.
If you want merged count tables you should do this:
mdat <- do.call(cbind,lapply(dat,assay))
Where row.names are Ensembl gene IDs and col.names are the SRR accessions.
Then run your table writing command.
-
If you want the coordinates of your genes then do this to make a bed with the genomic locations:
library(rtracklayer)
export.bed(rowRanges(dat[[1]]),'gene_coords.bed')
answered Feb 12 at 17:10
storystory
758211
$endgroup$
add a comment |
4
$begingroup$
You can't cbind a bunch of obscure object types.
If you want merged count tables you should do this:
mdat <- do.call(cbind,lapply(dat,assay))
Where row.names are Ensembl gene IDs and col.names are the SRR accessions.
Then run your table writing command.
-
If you want the coordinates of your genes then do this to make a bed with the genomic locations:
library(rtracklayer)
export.bed(rowRanges(dat[[1]]),'gene_coords.bed')
answered Feb 12 at 17:10
storystory
758211
$endgroup$
add a comment |
4
4
4
$begingroup$
You can't cbind a bunch of obscure object types.
If you want merged count tables you should do this:
mdat <- do.call(cbind,lapply(dat,assay))
Where row.names are Ensembl gene IDs and col.names are the SRR accessions.
Then run your table writing command.
-
If you want the coordinates of your genes then do this to make a bed with the genomic locations:
library(rtracklayer)
export.bed(rowRanges(dat[[1]]),'gene_coords.bed')
answered Feb 12 at 17:10
storystory
758211
$endgroup$
You can't cbind a bunch of obscure object types.
If you want merged count tables you should do this:
mdat <- do.call(cbind,lapply(dat,assay))
Where row.names are Ensembl gene IDs and col.names are the SRR accessions.
Then run your table writing command.
-
If you want the coordinates of your genes then do this to make a bed with the genomic locations:
library(rtracklayer)
export.bed(rowRanges(dat[[1]]),'gene_coords.bed')
answered Feb 12 at 17:10
storystory
758211
answered Feb 12 at 17:10
storystory
758211
answered Feb 12 at 17:10
storystory
758211
answered Feb 12 at 17:10
storystory
758211
758211
add a comment |
add a comment |
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1
$begingroup$
What is the class of mdat? Did you try
is(mdat)? What did you get?$endgroup$
– llrs
Feb 12 at 16:14
$begingroup$
@IIrs Hi I got this after this step [1] "RangedSummarizedExperiment" "SummarizedExperiment" "Vector" [4] "Annotated"
$endgroup$
– priya
Feb 12 at 16:15
1
$begingroup$
Great, see how fast you got your answer when you provided enough details, remember to include all the relevant details next time! Glad you found how to solve the problem
$endgroup$
– llrs
Feb 13 at 9:31