export_pval_igv: Export the p-values for comparisons of interest to visualize...

In SingerLab/gac: Genetic Analysis of Cells

Export the p-values for comparisons of interest to visualize in IGV

Description

Export the p-values for comparisons of interest to visualize in IGV

Usage

export_pval_igv(
  cnr,
  pval.column,
  outdir = ".",
  outfile.prefix,
  extension = ".logistic",
  na.value = "1",
  print.output = FALSE
)

Arguments

cnr	a cnr bundle
pval.column	column to export
outdir	output directory, default is "."
outfile.prefix	basename of file
extension	extesion compatible with IGV. Any of ".linear", ".logistic", ".assoc", ".qassoc", ".gwas". Default ".logistic"
na.value	value to give to NA, default 1 (i.e. p-value = 1)
print.output	print output on console as an object list with bin.pvalues and gene.pvalues

Value

Exports p-values from an analysis into two files, one containing "bin" level p-values, and another containing "gene" level p-values in IGV's GWAS format.

Bin-level p-values are expanded to all genes within each bin, such that the user can visualize the bin blocks with added resolution.

By default, any p-values with NA are converted to 1. These can arise in monomorphic regions of the genome and don't have an association to the phenotype.

References

https://software.broadinstitute.org/software/igv/GWAS

SingerLab/gac documentation built on March 23, 2024, 5:15 a.m.