peakAnno is a R package to annotate genomic regions (peaks) called/defined from different High-throughput sequencing data, including ChIP-seq, ATAC-seq and MeRIP-seq.
You can install the development version of peakAnno like so:
devtools::install_github("https://github.com/BioEpi/peakAnno")This is a basic example which shows you how to solve a common problem:
Write a reproducible example hereafter to explain how to use your package.
library(peakAnno)
## basic example code
peakAnno(GTF,organism,up,down,peaktype,bedfile,outpath,outfile) GTF: GTF files are available from https://www.gencodegenes.org/.
organism: the names of specie, such as homo sapiens and Mus
musculus.
up: the distance to the upstream of transcription start sites.
default value is 2000.
down: the distance to the downstream of transcription start sites.
default value is 0.
peaktype: what kind of sequencing data are used to call peaks.
default value is ‘m6A’.
bedfile: the name of peaks. The bed file includes chromosome, start,
end and strand (+/-/.). It is better to provide the absolute path of the
file.
| chr | start | end | strand |
|---|---|---|---|
| chr1 | 1000 | 1200 | + |
| chr1 | 1300 | 1500 | + |
| chr1 | 2000 | 2200 | + |
| chr1 | 2800 | 3200 | + |
| chr1 | 5000 | 5150 | + |
| chr1 | 6000 | 6350 | + |
outpath: the path is used to save the results.
outfile: the file name is used to save the results.
- Here the entire genome is separated to gene promoter/5’UTR/CDS/exon/intron/3’UTR.
- protein-coding genes have the following features: gene promoter/5’UTR/CDS/intron/3’UTR.
- non-coding genes have the following features: gene promoter/5’UTR/exon/intron/3’UTR.
- If your peak file is generated from ATAC-seq/ChIP-seq/Cut&Tag and peaks may be assigned to protein-coding genes, these peaks may be located in: gene promoter/5’UTR/CDS/intron/3’UTR. If peaks may be assigned to non-coding genes, these peaks may be located in: gene promoter/5’UTR/exon/intron/3’UTR.
- If your peak file is generated from MeRIP-seq, and peaks may be assigned to protein-coding genes, these peaks may be located in: gene promoter/5’UTR/CDS/3’UTR, If peaks may be assigned to non-coding genes, these peaks may be located in: gene promoter/5’UTR/exon/3’UTR.