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"









share|improve this question











$endgroup$








  • 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
















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"









share|improve this question











$endgroup$








  • 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














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"









share|improve this question











$endgroup$




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






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited Feb 13 at 9:32









llrs

3,2831632




3,2831632










asked Feb 12 at 15:41









priyapriya

324




324








  • 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














  • 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








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










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')





share|improve this answer









$endgroup$













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    1 Answer
    1






    active

    oldest

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    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')





    share|improve this answer









    $endgroup$


















      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')





      share|improve this answer









      $endgroup$
















        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')





        share|improve this answer









        $endgroup$



        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')






        share|improve this answer












        share|improve this answer



        share|improve this answer










        answered Feb 12 at 17:10









        storystory

        674110




        674110






























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