Dear community members,
I am new and relatively inexperienced with R and/or this forum so please be patient with my input. I am trying to download gene and exon annotation for human (hg19) and convert it to GenomicRanges object. I am performing the analysis in Windows10,64bit / Rstudio using a Bioconductor package called MetaseqR. It was working fine till I updated to R3.4.3. In brief I have installed the following :
R version 3.4.3, 64bit, Bioconductor version 3.6 [BiocInstaller 1.28.0], GenomicRanges 1.30.1 [installed from source, Rtools installed in the system-also tried binary 1.30.0 with no effect)
It seems to download the annotation but immediately I get the following error message :
Downloading gene annotation for hg19... Downloading exon annotation for hg19... Converting annotation to GenomicRanges object...Error in .find_start_end_cols(df_colnames0, start.field0, end.field0) : cannnot determine start/end columns
Tried downgrading to R3.4.2, R3.4.1 etc to no effect. Tried to run through R gui again the same...Please advice, I am desperate!