eSNPsEnrichmentAnalysis: Functional Enrichment of eQTL SNPs

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

Functional Enrichment of eQTL SNPs

Description

eQTL SNPs as input: for eSNP enrichment analysis, first, for each gene/transcript, we selected associated eSNPs as foreground (F) and SNPs within the 1Mb window around the TSS as background (B) SNP 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

eSNPsEnrichmentAnalysis(
  eQTL,
  TranscriptName,
  windowSize,
  FDRthreshold,
  BackendData_GenomicFeatures,
  BackendData_ChromatinStates,
  SNPs
)

Arguments

eQTL	eQTL profile including the following headers: seqnames, SNP_POS, SNP_POS, SNP_ID, gene_id
TranscriptName	Gene or isoform Ensembl ID
windowSize	window around the TSS (e.g. 1000000)
FDRthreshold	FDR threshold (e.g. 0.001)
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
SNPs	List of all SNPs in human genome

Value

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

Author(s)

Isar Nassiri, Benjamin Fairfax

Examples

data(eQTL)
data(BackendData_GenomicFeatures)
data(BackendData_ChromatinStates)
data(SNPs)
eSNPsEnrichmentAnalysis(eQTL, TranscriptName = 'ENSG00000168310', windowSize=1000000, FDRthreshold = 0.001, BackendData_GenomicFeatures, BackendData_ChromatinStates, SNPs)

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