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

View source: R/logistic_reg_histology.R

export_pval_igvR Documentation

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 Oct. 14, 2022, 4:09 a.m.