Files for CHIPseeker analysis
Could someone please explain to me what files I need to have to do the CHIPseeker analysis? For example:
peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000),
TxDb=txdb, annoDb="org.Hs.eg.db")
What is that txdb file? I understand I have to annotate .bed file I have first? Kindly help.
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TxDbR objects store information about transcripts and genes for a genome. Bioconductor has TxDb libraries for many organisms, such as humans. You can also turn a GTF/GFF file into a TxDb object usingGneomicFeatures::makeTxDbFromGFF. You can read more in the GenomicFeatures vignette here.