FunciSNP: Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FunciSNP")
AuthorSimon G. Coetzee <simon@simoncoetzee.com> and Houtan Noushmehr, PhD <houtan@usp.br>
Bioconductor views Annotation DataImport DataRepresentation Infrastructure SequenceMatching
Date of publicationNone
MaintainerSimon G. Coetzee <simon@simoncoetzee.com>
LicenseGPL-3
Version1.18.0
http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/

View on Bioconductor

Functions

AFR.overlapping.snps.geno Man page
AFR.overlapping.snps.geno,TagSNP-method Man page
alt.allele Man page
alt.allele<- Man page
alt.allele<-,CorrelatedSNPs-method Man page
alt.allele,CorrelatedSNPs-method Man page
alt.allele<-,TagSNP-method Man page
alt.allele,TagSNP-method Man page
AMR.overlapping.snps.geno Man page
AMR.overlapping.snps.geno,TagSNP-method Man page
ASN.overlapping.snps.geno Man page
ASN.overlapping.snps.geno,TagSNP-method Man page
chr Man page
chr<- Man page
chr<-,CorrelatedSNPs-method Man page
chr,CorrelatedSNPs-method Man page
chr<-,TagSNP-method Man page
chr,TagSNP-method Man page
class:CorrelatedSNPs Man page
class:TagSNP Man page
correlated.snps Man page
correlated.snps<- Man page
CorrelatedSNPs Man page
CorrelatedSNPs-class Man page
correlated.snps<-,TagSNP-method Man page
correlated.snps,TagSNP-method Man page
EUR.overlapping.snps.geno Man page
EUR.overlapping.snps.geno,TagSNP-method Man page
FunciSNPAnnotateSummary Man page
FunciSNPbed Man page
FunciSNP.data Man page
FunciSNPidsFromSummary Man page
FunciSNP-package Man page
FunciSNPplot Man page
FunciSNPsummaryOverlaps Man page
FunciSNPtable Man page
genotype Man page
genotype<- Man page
genotype<-,TagSNP-method Man page
genotype,TagSNP-method Man page
getFSNPs Man page
glioma Man page
overlapping.features Man page
overlapping.features<- Man page
overlapping.features<-,CorrelatedSNPs-method Man page
overlapping.features,CorrelatedSNPs-method Man page
pop.genotype Man page
pop.genotype<- Man page
pop.genotype<-,CorrelatedSNPs-method Man page
pop.genotype,CorrelatedSNPs-method Man page
population Man page
population<- Man page
population<-,TagSNP-method Man page
population,TagSNP-method Man page
position Man page
position<- Man page
position<-,CorrelatedSNPs-method Man page
position,CorrelatedSNPs-method Man page
position<-,TagSNP-method Man page
position,TagSNP-method Man page
ref.allele Man page
ref.allele<- Man page
ref.allele<-,CorrelatedSNPs-method Man page
ref.allele,CorrelatedSNPs-method Man page
ref.allele<-,TagSNP-method Man page
ref.allele,TagSNP-method Man page
show,TagSNP-method Man page
show,TSList-method Man page
snpid Man page
snpid<- Man page
snpid<-,CorrelatedSNPs-method Man page
snpid,CorrelatedSNPs-method Man page
snpid<-,TagSNP-method Man page
snpid,TagSNP-method Man page
summary,TSList-method Man page
TagSNP Man page
TagSNP-class Man page
TSList Man page
TSList-class Man page
yafsnp.dprime Man page
yafsnp.dprime<- Man page
yafsnp.dprime<-,TagSNP-method Man page
yafsnp.dprime,TagSNP-method Man page
yafsnp.pvalue Man page
yafsnp.pvalue<- Man page
yafsnp.pvalue<-,TagSNP-method Man page
yafsnp.pvalue,TagSNP-method Man page
yafsnp.rsq Man page
yafsnp.rsq<- Man page
yafsnp.rsq<-,TagSNP-method Man page
yafsnp.rsq,TagSNP-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/classes.R R/funcisnp.R
build
build/vignette.rds
data
data/datalist
data/glioma.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/FunciSNP_vignette.R
inst/doc/FunciSNP_vignette.Rnw
inst/doc/FunciSNP_vignette.pdf
inst/extdata
inst/extdata/TFBS_Nrsf_U87.bed
inst/extdata/TFBS_Pol2_U87.bed
inst/extdata/glioma.snp
man
man/CorrelatedSNPs-class.Rd man/FunciSNP-package.Rd man/FunciSNPAnnotateSummary.Rd man/FunciSNPbed.Rd man/FunciSNPidsFromSummary.Rd man/FunciSNPplot.Rd man/FunciSNPsummaryOverlaps.Rd man/FunciSNPtable.Rd man/TSList-class.Rd man/TagSNP-class.Rd man/getFSNPs.Rd
vignettes
vignettes/FunciSNP_vignette.Rnw
vignettes/UCSC_genomeviewer_glioma.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.