jaguar_plotqtl {JAGUAR} | R Documentation |
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.
jaguar_plotqtl(geneID,snpID,gene.chr,gene.pos,snp.chr,snp.pos,scores,chroms=1:22)
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) |
Chaitanya R. Acharya Maintainer: Chaitanya Acharya<c.acharya@duke.edu>
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
jaguar_gwa,jaguar_process,jaguar_slice,jaguar_cis,jaguar_sim
## 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)