Question: Files for CHIPseeker analysis
gravatar for ja4123
6 weeks ago by
ja41230 wrote:

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="")

What is that txdb file? I understand I have to annotate .bed file I have first? Kindly help.

R chip-seq chipseeker • 167 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by ja41230

TxDb R 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 using GneomicFeatures::makeTxDbFromGFF. You can read more in the GenomicFeatures vignette here.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by rpolicastro4.0k
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