GetPromoterAnno: Retrive promoter annotation from UCSC database

In Liuy12/MBDDiff: MBDDiff for processing MBDcap-seq datasets

Description

Retrive promoter annotation of user-specified organism from UCSC database

Usage

GetPromoterAnno(organism, save = FALSE, Dir = NULL)

Arguments

organism	the organism you want to extract promoter annotation
save	Logical value indicating whether you want to save the output locally
Dir	If save is set to TRUE, you also need to provide directory that you would like to save the output to.

Details

This function firstly retrive 'refflat' table information from UCSC database through their MySQL server. Then for each gene, records with the same TSS are collapsed. Genes with multiple records are marked by the same gene name followed by '#' and a number.

Value

A data.frame containing promoter annotation information

geneName	Official gene symbols
chrom	chromsome number
strand	The strand of the gene
txStart	Start location of transcripts
txEnd	End location of transcripts

Author(s)

Yuanhang Liu

References

https://github.com/Liuy12/MBDDiff

Examples

## Not run: 
    Promoter_anno <- GetPromoterAnno('hg19')
    
## End(Not run)

Liuy12/MBDDiff documentation built on May 7, 2019, 2 p.m.