R: 2D pQTL plot

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]