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

## Documentation for package ‘FunciSNP’ version 1.31.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

FunciSNP-package | Functional Identification of SNPs with Phenotype by Coincidence with Chromatin Biofeatures
AFR.overlapping.snps.geno | Class '"TagSNP"'
AFR.overlapping.snps.geno-method | Class '"TagSNP"'
alt.allele | Class '"TagSNP"'
alt.allele-method | Class '"CorrelatedSNPs"'
alt.allele-method | Class '"TagSNP"'
alt.allele<- | Class '"TagSNP"'
alt.allele<--method | Class '"CorrelatedSNPs"'
alt.allele<--method | Class '"TagSNP"'
AMR.overlapping.snps.geno | Class '"TagSNP"'
AMR.overlapping.snps.geno-method | Class '"TagSNP"'
ASN.overlapping.snps.geno | Class '"TagSNP"'
ASN.overlapping.snps.geno-method | Class '"TagSNP"'
chr | Class '"TagSNP"'
chr-method | Class '"CorrelatedSNPs"'
chr-method | Class '"TagSNP"'
chr<- | Class '"TagSNP"'
chr<--method | Class '"CorrelatedSNPs"'
chr<--method | Class '"TagSNP"'
class:CorrelatedSNPs | Class '"CorrelatedSNPs"'
class:TagSNP | Class '"TagSNP"'
correlated.snps | Class '"TagSNP"'
correlated.snps-method | Class '"TagSNP"'
correlated.snps<- | Class '"TagSNP"'
correlated.snps<--method | Class '"TagSNP"'
CorrelatedSNPs | Class '"CorrelatedSNPs"'
CorrelatedSNPs-class | Class '"CorrelatedSNPs"'
EUR.overlapping.snps.geno | Class '"TagSNP"'
EUR.overlapping.snps.geno-method | Class '"TagSNP"'
FunciSNP.data | Functional Identification of SNPs with Phenotype by Coincidence with Chromatin Biofeatures
FunciSNPAnnotateSummary | Genomic Annotation of YAFSNPs.
FunciSNPbed | Creates a BED file to view YAFSNPs in your favorite genome browser
FunciSNPidsFromSummary | coming soon.
FunciSNPplot | FunciSNPplot to visualize YAFSNP summary.
FunciSNPsummaryOverlaps | Summarizes FunciSNP results by overlaps
FunciSNPtable | Will output a summary report from FunciSNP at specified Rsquare cut-offs.
genotype | Class '"TagSNP"'
genotype-method | Class '"TagSNP"'
genotype<- | Class '"TagSNP"'
genotype<--method | Class '"TagSNP"'
getFSNPs | Functional Identification of SNPs with Phenotype by Coincidence with Chromatin Biofeatures
glioma | Functional Identification of SNPs with Phenotype by Coincidence with Chromatin Biofeatures
overlapping.features | Class '"CorrelatedSNPs"'
overlapping.features-method | Class '"CorrelatedSNPs"'
overlapping.features<- | Class '"CorrelatedSNPs"'
overlapping.features<--method | Class '"CorrelatedSNPs"'
pop.genotype | Class '"CorrelatedSNPs"'
pop.genotype-method | Class '"CorrelatedSNPs"'
pop.genotype<- | Class '"CorrelatedSNPs"'
pop.genotype<--method | Class '"CorrelatedSNPs"'
population | Class '"TagSNP"'
population-method | Class '"TagSNP"'
population<- | Class '"TagSNP"'
population<--method | Class '"TagSNP"'
position | Class '"TagSNP"'
position-method | Class '"CorrelatedSNPs"'
position-method | Class '"TagSNP"'
position<- | Class '"TagSNP"'
position<--method | Class '"CorrelatedSNPs"'
position<--method | Class '"TagSNP"'
ref.allele | Class '"TagSNP"'
ref.allele-method | Class '"CorrelatedSNPs"'
ref.allele-method | Class '"TagSNP"'
ref.allele<- | Class '"TagSNP"'
ref.allele<--method | Class '"CorrelatedSNPs"'
ref.allele<--method | Class '"TagSNP"'
show-method | Class '"TSList"'
show-method | Class '"TagSNP"'
snpid | Class '"TagSNP"'
snpid-method | Class '"CorrelatedSNPs"'
snpid-method | Class '"TagSNP"'
snpid<- | Class '"TagSNP"'
snpid<--method | Class '"CorrelatedSNPs"'
snpid<--method | Class '"TagSNP"'
summary-method | Class '"TSList"'
TagSNP | Class '"TagSNP"'
TagSNP-class | Class '"TagSNP"'
TSList | Class '"TSList"'
TSList-class | Class '"TSList"'
yafsnp.dprime | Class '"TagSNP"'
yafsnp.dprime-method | Class '"TagSNP"'
yafsnp.dprime<- | Class '"TagSNP"'
yafsnp.dprime<--method | Class '"TagSNP"'
yafsnp.pvalue | Class '"TagSNP"'
yafsnp.pvalue-method | Class '"TagSNP"'
yafsnp.pvalue<- | Class '"TagSNP"'
yafsnp.pvalue<--method | Class '"TagSNP"'
yafsnp.rsq | Class '"TagSNP"'
yafsnp.rsq-method | Class '"TagSNP"'
yafsnp.rsq<- | Class '"TagSNP"'
yafsnp.rsq<--method | Class '"TagSNP"'