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

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Documentation for package ‘FunciSNP’ version 1.18.0

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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"'