import_hap: Import hapResult/hapSummary

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

Import hapResult/hapSummary

Description

This function could be used for import hap result or hap summary result. The type of returned object is decided by input file, see details.

Usage

import_hap(file, type = "auto", ...)

Arguments

file	hapSummary or hapResult file path.
type	the content type of imported file, should be one of c("hapResult", "hapSummary")
...	extras will pass to read.delim()

Details

The hap result and hap summary result have common features. The common features of these two types are: First four rows contains extra information: CHR, POS, INFO and ALLELE Hap names were in the first column. The differences are: Hap summary result have a freq column while hap result not. Rows represent haplotypes in hap summary result, while rows represent accessions in hap result. In addtion, the accessions of each haplotype in hap summary result were separated by ";".

Value

hapSummary or hapResult

Examples

oldDir <- getwd()
temp_dir <- tempdir()
if(! dir.exists(temp_dir))
  dir.create(temp_dir)
setwd(temp_dir)
data("geneHapR_test")
write.hap(hapResult, file = "test.pheno.txt", sep = "\t")
hap <- import_hap("test.pheno.txt")
hap
setwd(oldDir)

geneHapR documentation built on May 29, 2024, 11:59 a.m.