pqtl2dplot {gap}R Documentation

2D pQTL plot

Description

2D pQTL plot

Usage

pqtl2dplot(
  d,
  chrlen = gap::hg19,
  snp_name = "SNP",
  snp_chr = "Chr",
  snp_pos = "bp",
  gene_chr = "p.chr",
  gene_start = "p.start",
  gene_end = "p.end",
  protein = "p.target.short",
  gene = "p.gene",
  lp = "log10p",
  cis = "cis",
  plot = TRUE,
  cex = 0.6
)

Arguments

d

Data to be used.

chrlen

lengths of chromosomes for specific build: hg18, hg19, hg38.

snp_name

variant name.

snp_chr

variant chromosome.

snp_pos

variant position.

gene_chr

gene chromosome.

gene_start

gene start position.

gene_end

gene end position.

protein

protein name.

gene

gene name.

lp

log10(p).

cis

cis variant when TRUE.

plot

to plot when TRUE.

cex

extension factor.

Value

positional information.

Examples

## Not run: 
INF <- Sys.getenv("INF")
d <- read.csv(file.path(INF,"work","INF1.merge.cis.vs.trans"),as.is=TRUE)
r <- pqtl2dplot(d)

## End(Not run)
[Package gap version 1.2.3-6 Index]