read_happy: Load a hap.py results directory

In Illumina/happyR: Load hap.py results into R

Description

Read a directory of hap.py output files into an R data structure.

Usage

read_happy(happy_prefix, lazy = TRUE, quietly = FALSE)

Arguments

happy_prefix	hap.py output prefix (and path)
lazy	store lesser-used output as unevaluated promises rather than reading everything at once
quietly	inhibit logging messages as files are loaded

Value

A list structure containing hap.py output

Examples

## Not run: 
# run hap.py from commandline:
#  hap.py truth.vcf query.vcf -o /output/path/prefix

# load result into R
happy <- read_happy('/output/path/prefix')

## End(Not run)

# load demo data supplied with package
happy_input <- system.file("extdata", "happy_demo.summary.csv", package = "happyR")
happy_prefix <- sub(".summary.csv", "", happy_input)

hapdata <- read_happy(happy_prefix)
print(hapdata)

Illumina/happyR documentation built on July 12, 2019, 7:57 p.m.