prune.genes: Prune markers by physical position

In tobyjohnson/gtx: Genetics ToolboX

Description

Selects subset of markers so that all excluded markers are within threshold physical genes of included markers.

Usage

prune.genes(chr, pos, genetable, genes, win.size = 10000)

Arguments

chr	Chromosome
pos	Position
genetable	A data frame of a UCSC genome browser table
genes	Genes
win.size	Distance threshold

Details

To write.

genetable could be the refgene or GENCODE table from UCSC. It must have columns “chrom”, “txStart”, “txEnd”, “name2”.

Value

A vector of true/false.

Author(s)

Toby Johnson [e-mail]

Examples

data(gencode14.UGT1A1)
markers <- data.frame(CHROM = paste("chr", c(rep(1, 1000), rep(2, 3000)), sep = ""),
                      POS = sort(runif(4000, 233000000, 235000000)),
		      pval = runif(4000, 1e-5, 1))
## within 5kb of either of two genes
markers$nearGene <- prune.genes(markers$CHROM, markers$POS, gencode14.UGT1A1, c("DNAJB3", "HJURP"), 5000)
with(markers, table(CHROM, nearGene))

leftrightpos <- c(234568893, 234781945)
plot.new()
plot.window(leftrightpos, c(-5, 5))
abline(h = 0, col = "grey")
gene.draw(2, leftrightpos[1], leftrightpos[2], gencode14.UGT1A1, genesep = 5000)
axis(1, at = pretty(leftrightpos * 1e-6)*1e6, labels = pretty(leftrightpos * 1e-6))
title(xlab = "chr2 genomic position (Mb)")
axis(2, at = 0:5, las = 1)
box()

with(markers, points(POS, -log10(pval), pch = 21, bg = ifelse(nearGene, "red", "grey")))

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.