I'm trying to do COG and GSEA with the R package BOG, and couldn't find information about problem solving for the package.
I'm working on RNAseq data from various Brucella species, and BOG seems to be the only package that deals with bacteria.
I installed the package and followed its documentation:
> dataframe <- read.table('test.txt', header = TRUE, sep = '\t') > BOG(dataframe, data.type="pval", 'brucella')
which caused as error:
Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column
so I tied
> BOG(dataframe, data.type="pval", 'brucella')
which yielded the error
Error in BOGest(data, data.type, cog.file, hg.thresh = hg.thresh, gsea = gsea, : BOG : The fisrt element of data frame should be character
If someone has experience in working with this package, I'd love to get some suggestions. If anyone has an idea about another package I could use, I'd be happy for your suggestions too.