Error in as.vector(x) : no method for coercing this S4 class to a vector
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")
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benformatics
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pr2009 •
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pr2009 •
1 answer
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 write.table(mdat, "recount_mdat.csv") 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')
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Do you understand the steps that you are doing? Your error should be in "mdat <- do.call(cbind, dat)" rather than the following step of write.table.
Hint: what does class(rse_gene) give you? if it not a vector, you can't run your cbind with do.call because cbind expects a vector (or matrix)
Hello priyankaraina10!
We believe that this post does not fit the main topic of this site.
Not a bioinformatics Q and cross-posted on SE https://bioinformatics.stackexchange.com/questions/7010/error-in-as-vectorx-no-method-for-coercing-this-s4-class-to-a-vector
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