Files for CHIPseeker analysis
0
0
Entering edit mode
3.9 years ago
ja4123 ▴ 30

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.

chipseeker chip-seq r • 1.3k views
ADD COMMENT
1
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2057 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6