problem while knitting .rmd file

[mz_huji]

Hi,

Im doing a class assignment and have an R notebook which I need to knit to HTML. I always knitted with the button and it always worked fine until now.

#Loading package and files
library(GenomicRanges)
EPlinks <- GRanges(all_links.xlsx)
Linked_gene <- GRanges(genes_linked)
TADcalls_HepG2 <- GRanges(HepG2_ENCODE3_raw_domains)
TADcalls_GM12878 <- GRanges(GM12878_Rao_2014_raw_TADs)
TADcalls_Pan <- GRanges(Pancreas_Schmitt2016_raw_TADs)

those are the first code lines, and this is the error im getting:

I already updated R, RStudio and the different packages and nothing seems to work.

Thanks in advance for any help!

[technocrat]

@mz_huji

EPlinks <- GRanges(all_links.xlsx)

The function GRanges needs an object in namespace as an argument. If all_links.xlsx is a file, instead, it needs to be quoted

 EPlinks <- GRanges("all_links.xlsx")

and the file needs to be in the working directory.

[mz_huji]

Hi,

that didnt help. I did it to all the files i was using and it didnt help.
Im in the working directory.

what might cause this?

[StatSteph]

When you knit a Rmd file, it makes the working directory the same as wherever the Rmd file is saved so either save the xlsx files in the same folder as the Rmd file, use a full path, or take a look at the here package to use relative paths from the Rmd file a bit easier.