tntplot2: detailed plot
In vjcitn/tnt4dn8: TnT applications with GWAS in dn8 format

tntplot2

R Documentation

detailed plot

Description

detailed plot

Usage

tntplot2(
  tab,
  snpcolor = "lightblue",
  genecolor = "darkgreen",
  txcolor = "darkred",
  GT = NULL,
  tt = NULL,
  maxp = 0.1,
  trunc_mlp = 300
)

Arguments

`tab`	data.frame
`snpcolor`	character(1)
`genecolor`	character(1)
`txcolor`	character(1)
`GT`	defaults to NULL, otherwise a GeneTrackFromTxDb-like object from TnT
`tt`	defaults to NULL, otherwise a TxTrackFromTxDb-like object from TnT
`maxp`	numeric(1) if non-NULL loci with p-values greater than this are excluded
`trunc_mlp`	numeric(1) defaults to 300, -log10p greater than this are reset to this value

Examples

if (requireNamespace("TnT") & requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene")) {
data(gtex_b38_lung_chr20_exc)
cands = avail_syms_gtex()
cands
chk2 = gtex_b38_lung_chr20_exc |> filter_sym(cands[3], radius=5e4) |> as.data.frame()
print(tntplot2(chk2))
}

vjcitn/tnt4dn8 documentation built on Sept. 10, 2022, 11:17 a.m.