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