querySNPsEnrichmentAnalysis: Single query SNP enrichment
In isarnassiri/FEVV: FEVV: Functional Enrichment of Genomic Variants and Variations

Description Usage Arguments Value Author(s) Examples

View source: R/FEVV.R

a query SNP as the input: a query SNP as input: first, the 1MB window is defined for the query SNP, and the relevant variants captured from the 1000 genomes data in the European population background. Next, we split the SNPs based upon a LD (R?? = 0.8 and MAF = 0.01) to foreground (query SNP and its LD proxies) and background SNPs sets. We used the number of overlaps of foreground (f) and background (b) SNP sets in the genomic feature or chromatin state and calculate the enrichment score (z-score and odds ratio).

querySNPsEnrichmentAnalysis(
  SNP,
  mafThreshold,
  windowSize,
  BackendData_GenomicFeatures,
  BackendData_ChromatinStates,
  vcfMetaData,
  vcfPATH
)

`SNP`	a query SNP
`mafThreshold`	minor allele frequency (MAF) threshold
`windowSize`	window around the TSS (e.g. 1000000)
`BackendData_GenomicFeatures`	fifteen-core chromatin states from https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/coreMarks/jointModel/final/download/
`BackendData_ChromatinStates`	10 genomic features from the biomaRt (Ensembl) and UCSC
`vcfMetaData`	meta data of 1000 Genomes project (phase3) including 'sample', 'pop', 'super_pop', and 'gender' header
`vcfPATH`	Pathe to the vcf file.

You can find the results in R object under title of 'RESULTsGenomicFeatures' and 'RESULTsChromatinState'.

Isar Nassiri, Benjamin Fairfax

data(BackendData_GenomicFeatures)
data(BackendData_ChromatinStates)
Destiny_Folder <- system.file(package = "FEVV")
querySNPsEnrichmentAnalysis(SNP = 'rs13149699', mafThreshold = 0.039, windowSize = 1000000, BackendData_GenomicFeatures, BackendData_ChromatinStates, vcfMetaData = system.file("extdata", "Genotyping1000_samples_metatadata.txt", package="FEVV"), vcfPATH = 'http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/ALL.chr4.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz' )