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  • #58

Closed
Open
Created Jun 27, 2019 by herseman@hersemanOwner

dge_workflow: error message because gtf_file did not exist

ran featcounts_deseq_mf.R without specifying the gtf file and got the following error message:

Warning message:
package ‘GenomicFeatures’ was built under R version 3.5.3
> ## horrible hack to avoid masking of dplyr::sel
> select <- dplyr::select
>
> ## import gtf
> # if(!file.exists(gene.model)) stop(paste("GTF File:", gene.model, " does NOT exist. Run with: \n", runstr))
>
> gtf <- import.gff(
+     gtf_file,
+     format = "gtf",
+     feature.type = "exon"
+ )
Error in (function (classes, fdef, mtable)  :
unable to find an inherited method for function ‘import’ for signature ‘"NULL", "character", "character"’
Calls: import.gff -> import.gff -> import -> <Anonymous>
Execution halted
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