basic2: simple demo for a table like those produced by Ahmed

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

simple demo for a table like those produced by Ahmed

Description

simple demo for a table like those produced by Ahmed

Usage

basic2(
  table,
  trackName = "demo",
  pval.col = 10,
  chrom.col = 1,
  pos.col = 3,
  genome = "hg38",
  windowTitle = "simple demo",
  ...
)

Arguments

table	data.frame with p-values, chr, pos in specified columns with known integer indices
trackName	character(1)
pval.col	numeric index giving column number of table holding p-values
chrom.col	numeric index giving column number of table holding numeric chromosome
pos.col	numeric index giving column number of table holding numeric bp position
genome	character(1) defaults to "hg38"
windowTitle	character(1) defaults to "simple demo"
...	passed to igvR::GWASTrack

Examples

data(pax_demo)
# eliminate "uninteresting" loci
pax_demo_filt = pax_demo[pax_demo$P < .1,]
basic2(table=pax_demo_filt)

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