I'm new to R, but am trying to analyze 2 ChIP-Seq data sets. I have been following along with several ChIPpeakAnno guides and I am running into a problem I can't figure out. I have managed to find overlapping peaks, but when I go to annotate them I run into the following problem:
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> annoData <- toGRanges(EnsDb.Hsapiens.v75, feature="gene")
Error in toGRanges(EnsDb.Hsapiens.v75, feature = "gene") :
No valid data passed in. For example a data frame as BED format
file with at least 3 fields in the order of: chromosome, start and end.
Optional fields are name, score and strand etc.
Please refer to http://genome.ucsc.edu/FAQ/FAQformat#format1 for details.