IdentifyBackground: Identify annotation for background noise
In Liuy12/MBDDiff: MBDDiff for processing MBDcap-seq datasets

Description Usage Arguments Details Value Author(s) References See Also Examples

Identify background regions based on

1	IdentifyBackground(organism, bed_path, binsize=100, promo_bed, cores=detectCores())

`organism`	Accession code for organism that you would like to extract information from. For a list of availabe organisms, please see `ShowAvailableOrg`
`bed_path`	Absolute path you wanna to save the internally generated bed file that is created by user-specified bin size
`binsize`	Bin size in bases to create a sliding window across the genome
`promo_bed`	The promoter annotation generated by `GetPromoterAnno`
`cores`	Number of cores used for parallel processing

To identify regions that potentially contribute to background noise, we built a 100 bp tiling window across the whole genome. In order to identify the regions for measuring background noise, we applied following procedures:

1. Filtering step: In all the 100 bp windows, exclude any window that resides in promoter regions, predicted CpG islands regions and windows that contains ambiguous bases (gaps)

Firstly, construct potentially functional regions to exclude from 100bp windows Then, extract sequence files for the newly constructed 100bp windows. The output fasta file will be used to calcualte GC content statistics in whole genome sliding windows: Finally, filter 100 bp windows by excluding those that intersect with functional elements 2. Construct preliminary background regions based on GC content: for each promoter region, identify 80 100bp windows nearby that has low in GC content (< 40

A data.frame that contains the following elements:

`chrom`	Chromsome number
`chromStart`	Chromsome Start coordinate
`chromEnd`	Chromsome End coordinate
`GC`	GC content
`proximity`	Distance to cloest gene
`geneName`	Cloest gene name

Yuanhang Liu

https://github.com/Liuy12/MBDDiff

Summerizebg

## Not run: 
    bed_100bp_bg <- IdentifyBackground(organism = 'hg19', bed_path = 'path/to/bed', binsize = 100, promo_bed = Promoter_anno, cores = 4)
  
## End(Not run)