querySNPsEnrichmentAnalysis: Single query SNP enrichment

In isarnassiri/FEVV: FEVV: Functional Enrichment of Genomic Variants and Variations

Single query SNP enrichment

Description

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).

Usage

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

Arguments

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.

Value

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

Author(s)

Isar Nassiri, Benjamin Fairfax

Examples

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' )

isarnassiri/FEVV documentation built on Oct. 30, 2024, 7:30 p.m.