GWASinspector (version 1.4.3)

run.inspector: Runs the Inspector algorithm on a list of GWAS result files

Description

This is the main function of the package, which runs the QC algorithm on GWAS result files. It requires an object of class '>Inspector which should be created by setup.inspector. Check the package vignette and tutorial for more details on this topic.

Usage

run.inspector(inspector, test.run = FALSE)

Arguments

inspector

An instance of '>Inspector class. Check setup.inspector for more details.

test.run

logical. If TRUE, only the first 1000 lines of each data file are loaded and analysed; plots and saving the cleaned output dataset are skipped. Default value is FALSE.

Value

Reports from running the algorithm on a single or a series of GWAS result files are generated and saved.

Examples

# NOT RUN {
# save a sample configuration file and edit it as required.
config.file <- get.config(tempdir())

# import the QC-configuration file into R.
job <- setup.inspector(config.file)

# check the generated object.
job

# run the generated object.
# This may take up to a couple of hours, depending on your PC and the size/number of files.
job <- run.inspector(job)

# view a brief summary about the result. report files and plots are already saved.
result.inspector(job)
# }
# NOT RUN {
# }