jaguar_plotqtl: Plotting the eQTL results

In cramanuj/JAGUAR: Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test Approach to Map Expression Quantitative Trait Loci (eQTL)

Description

Scatter plot displaying eQTL results with transcript location on the y-axis and SNP location on the x-axis. This plot is an implementation of ePlot function from Wei Sun's eMap R-package.

Usage

jaguar_plotqtl(geneID,snpID,gene.chr,gene.pos,snp.chr,snp.pos,scores,chroms=1:22)

Arguments

geneID	A vector indicating the genes to be mapped
snpID	A vector indicating the SNPs to be mapped
gene.chr	A vector indicating the chromosomal location of the genes to be mapped
gene.pos	A vector indicating the start site of all the genes on the Gene Chip
snp.chr	A vector indicating the chromosomal location of the SNPs to be mapped
snp.pos	A vector indicating the chromosomal location of all the SNPs on the SNP Chip
scores	A vector of p-values of each Gene-SNP pair
chroms	A vector indicating the number of chromosomes to me mapped. Usually, it is 1 to 22 (excluding X and Y chromosomes)

Author(s)

Chaitanya R. Acharya Maintainer: Chaitanya Acharya<[e-mail]>

References

eQTL analysis by Linear Model http://www.bios.unc.edu/~weisun/software/eMap.pdf

Chaitanya R. Acharya, Kouros Owzar, Janice M. McCarthy and Andrew S. Allen; Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. BMC Bioinformatics (2016) 17:257 DOI 10.1186/s12859-016-1123-5

See Also

jaguar_gwa,jaguar_process,jaguar_slice,jaguar_cis,jaguar_sim

Examples

## NOT RUN
### Read the annotation file of the Gene Chip
#genes = read.table("gene_annotation.txt",header=T,check.names=F)
#eChr = genes$Chromosome
#ePos = genes$StartSite
#
### Read the annotation file of the SNP Chip
#snps = read.table("snp_annotation.txt",header=F)
#mChr = snps$Chr
#mPos = snps$Pos
#
### Read the significant Gene-SNP pairs that are needed to be mapped
#out = jaguar_process(jaguar.out,threshold=0.05)
#
#geneID = match(out$Gene,genes$Probe_Id)
#markerID = match(out$SNP,snps$SNP_Id)
#scores = out$P.value
#chroms=1:22
#
#jaguar_plotqtl(geneID,snpID,gene.chr,gene.pos,snp.chr,snp.pos,scores,chroms)

cramanuj/JAGUAR documentation built on May 13, 2019, 10:55 p.m.