Question: Files for CHIPseeker analysis
0
gravatar for ja4123
6 weeks ago by
ja41230
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="org.Hs.eg.db")

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
1

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2092 users visited in the last hour
_