FunciSNPbed {FunciSNP} | R Documentation

## Creates a BED file to view YAFSNPs in your favorite genome browser

### Description

FunciSNPbed will output a BED file to a specified folder. The BED file is in standard UCSC Genome Browser format (http://genome.ucsc.edu/FAQ/FAQformat). Each tagSNP is colored black and each YAFSNP is colored red.

### Usage

    FunciSNPbed(dat, rsq, path = getwd(), filename = NULL)

### Arguments

`dat` | FunciSNP data.frame: `dat` is a data.frame object from FunciSNPAnnotateSummary. Need to run `FunciSNPAnnotateSummary` first.
`rsq` | an interger (0-1): `rsq` is the Rsquared cutoff used to subset.
`path` | a character: `path` is the path to the folder where to save the BED file. Default to getwd() or current working directory.
`filename` | a character: `filename` is the name of the BED file. If NULL, filename is 'FunciSNP_results_rsq.RSQ value.bed'

### Details

FunciSNPbed outputs a unique BED file which can be used to view in any genomic browser compatible with BED formats. To learn more about BED formats, see UCSC Genome Browser FAQ (http://genome.ucsc.edu/FAQ/FAQformat). Each tagSNP which is in LD to a corresponding YAFSNP overlapping at least one biofeature is colored black, while the YAFSNP is colored red. The initial position is provided by the first tagSNP and the first linked YAFSNP. We recommend using UCSC genome browser to view your BED files. This is useful so you can view all public and private tracks in relation to FunciSNP results.

### Value

BED file is outputed as a tab-deliminated file in the specified 'path' folder. See example below.

### Note

NA

### Author(s)

Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)

### References

SG. Coetzee, SK. Rhie, BP. Berman, GA. Coetzee and H. Noushmehr, FunciSNP: An R/Bioconductor Tool Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs., Nucleic Acids Research, In press, 2012 (doi:10.1093/nar/gks542).

### See Also

`getFSNPs`, `FunciSNPplot`, `FunciSNPAnnotateSummary`, `FunciSNPtable`, `FunciSNPbed`

### Examples

    ##
    data(glioma);
    glioma.anno <- FunciSNPAnnotateSummary(glioma);
    FunciSNPbed(glioma.anno, rsq=0.9);
    ####
    #Bed file "FunciSNP_results_rsq.0.9.bed" created successfully.
    #(See folder: "/home/houtan/Downloads/")
    #Total corSNP (RED):  15
    #Total tagSNP (BLK):  1

    #To view results, submit bed file as a
    #  custom track in UCSC Genome Browser (genome.ucsc.edu),

    #Now have fun with your new Func-y SNPs!!
    ####

[Package FunciSNP version 1.28.0 Index]