FunciSNP: Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Version 1.20.0

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

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
Version1.20.0
URL http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FunciSNP")

Getting started

Package overview

Popular man pages

FunciSNPAnnotateSummary: Genomic Annotation of YAFSNPs.
FunciSNP-package: Functional Identification of SNPs with Phenotype by...
FunciSNPplot: FunciSNPplot to visualize YAFSNP summary.
FunciSNPsummaryOverlaps: Summarizes FunciSNP results by overlaps
getFSNPs: Functional Identification of SNPs with Phenotype by...
TagSNP-class: Class '"TagSNP"'
TSList-class: Class '"TSList"'
See all...

All man pages Function index File listing

Man pages

CorrelatedSNPs-class: Class '"CorrelatedSNPs"'
FunciSNPAnnotateSummary: Genomic Annotation of YAFSNPs.
FunciSNPbed: Creates a BED file to view YAFSNPs in your favorite genome...
FunciSNPidsFromSummary: coming soon.
FunciSNP-package: Functional Identification of SNPs with Phenotype by...
FunciSNPplot: FunciSNPplot to visualize YAFSNP summary.
FunciSNPsummaryOverlaps: Summarizes FunciSNP results by overlaps
FunciSNPtable: Will output a summary report from FunciSNP at specified...
getFSNPs: Functional Identification of SNPs with Phenotype by...
TagSNP-class: Class '"TagSNP"'
TSList-class: Class '"TSList"'

Functions

AFR.overlapping.snps.geno Man page
AFR.overlapping.snps.geno,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
AnnotateSummary Source code
ChiSquaredPvalue Source code
CorrelatedSNPs Man page
CorrelatedSNPs-class Man page
CreateCorrelatedSNPs Source code
CreatePopulations Source code
CreateTagSNP Source code
EUR.overlapping.snps.geno Man page
EUR.overlapping.snps.geno,TagSNP-method Man page
FilterByFeatures Source code
FilteredLDTesting Source code
FunciSNP-package Man page
FunciSNP.data Man page
FunciSNPAnnotateSummary Man page Source code
FunciSNPbed Man page Source code
FunciSNPidsFromSummary Man page Source code
FunciSNPplot Man page Source code
FunciSNPsummaryOverlaps Man page Source code
FunciSNPtable Man page Source code
PullInVariants Source code
ReadRegionsFile Source code
SNPSummary Source code
ServerCheck Source code
TSList Man page Source code
TSList-class Man page
TagSNP Man page
TagSNP-class Man page
alt.allele Man page
alt.allele,CorrelatedSNPs-method Man page
alt.allele,TagSNP-method Man page
alt.allele<- Man page
alt.allele<-,CorrelatedSNPs-method Man page
alt.allele<-,TagSNP-method Man page
bedColors Source code
chr Man page
chr,CorrelatedSNPs-method Man page
chr,TagSNP-method Man page
chr<- Man page
chr<-,CorrelatedSNPs-method Man page
chr<-,TagSNP-method Man page
class:CorrelatedSNPs Man page
class:TagSNP Man page
correlated.snps Man page
correlated.snps,TagSNP-method Man page
correlated.snps<- Man page
correlated.snps<-,TagSNP-method Man page
genotype Man page
genotype,TagSNP-method Man page
genotype<- Man page
genotype<-,TagSNP-method Man page
getFSNPs Man page Source code
glioma Man page
overlapping.features Man page
overlapping.features,CorrelatedSNPs-method Man page
overlapping.features<- Man page
overlapping.features<-,CorrelatedSNPs-method Man page
pop.genotype Man page
pop.genotype,CorrelatedSNPs-method Man page
pop.genotype<- Man page
pop.genotype<-,CorrelatedSNPs-method Man page
population Man page
population,TagSNP-method Man page
population<- Man page
population<-,TagSNP-method Man page
position Man page
position,CorrelatedSNPs-method Man page
position,TagSNP-method Man page
position<- Man page
position<-,CorrelatedSNPs-method Man page
position<-,TagSNP-method Man page
ref.allele Man page
ref.allele,CorrelatedSNPs-method Man page
ref.allele,TagSNP-method Man page
ref.allele<- Man page
ref.allele<-,CorrelatedSNPs-method Man page
ref.allele<-,TagSNP-method Man page
setThemeWhite Source code
show,TSList-method Man page
show,TagSNP-method Man page
snpid Man page
snpid,CorrelatedSNPs-method Man page
snpid,TagSNP-method Man page
snpid<- Man page
snpid<-,CorrelatedSNPs-method Man page
snpid<-,TagSNP-method Man page
summary,TSList-method Man page
vlookup Source code
yafsnp.dprime Man page
yafsnp.dprime,TagSNP-method Man page
yafsnp.dprime<- Man page
yafsnp.dprime<-,TagSNP-method Man page
yafsnp.pvalue Man page
yafsnp.pvalue,TagSNP-method Man page
yafsnp.pvalue<- Man page
yafsnp.pvalue<-,TagSNP-method Man page
yafsnp.rsq Man page
yafsnp.rsq,TagSNP-method Man page
yafsnp.rsq<- Man page
yafsnp.rsq<-,TagSNP-method Man page
yapply Source code

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
FunciSNP documentation built on May 20, 2017, 9:50 p.m.

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