conditional: Perform simple stepwise conditional analysis for fine...

In liliulab/treemap: A Structured Approach to Fine Mapping of eQTL Variants

Perform simple stepwise conditional analysis for fine mapping.

Description

Perform simple stepwise conditional analysis for fine mapping.

Usage

conditional(
  input.folder = "./",
  pattern = "exp_geno.txt",
  output.folder = "./",
  mc.cores = 1
)

Arguments

input.folder:	The directory where input files are available. Default is the current working directory.
pattern:	A string that matches part of the input file names. This string shall be present in only input files, and absent from other file names in the same folder. Default is 'exp_geno.txt'.
output.folder:	The directory where output files and intermediate files are to be saved. If the specified directory does not exist, it will be automatically created. Default is the current working directory.
mc.cores:	The number of parallel processes that will be forked for batch processing. This is useful for multi-core desktops or server clusters. Default is 1.

Value

NULL The final fine mapping result is written to the file xx.treemap.out. The "locus" column indicates unique causal locus. The "rank" column indicates ranking of variants within each locus. Variants with rank of 1 are lead eVars at a locus. P-values and effects of lead eVars are in the "p" column and the "eff" column, respectively. Variants with rank >1 are ordered based on their linkage to the lead eVar at each locus, with r2 values shown in the "cor" column.

liliulab/treemap documentation built on May 11, 2023, 6:49 a.m.