dispersion_check: Effect estimates precision by sample size.

In GWAtoolbox: GWAS Quality Control

Description

Provides an assessment of the distribution of estimates' precision vs. the study sample size.

Usage

dispersion_check(script, sample_sizes = NULL, plot = TRUE)

Arguments

script	Name of a textual input file with processing instructions. The file should contain the names and locations of all GWAS data files to be processed along with basic information from each individual study, and instructions for the quality check.
sample_sizes	A vector with all study sample sizes.
plot	Logical value indicating if the diagnostic plot should be produced.

Details

The function uses CSV reports generated by gwasqc() function. As input it requires the same script as gwasqc() function and assumes that all the reports are in the current working directory. If the study sample size is missing from GWAS files, then the function has an optional parameter allowing to specify a vector with all study sample sizes. The function returns a data frame with the information extracted from the CSV reports and produces the diagnostic plot.

Author(s)

Cristian Pattaro, Daniel Taliun, Christian Fuchsberger

Examples

	

	# name of an input script
	script <- "GWASQC_script.txt"

	# load GWAtoolbox library
	library(GWAtoolbox)

	# show contents of the input script
	file.show(script, title=script)

	

	# run gwasqc() function
	gwasqc(script)
	
	# run dispersion_check() function
	Z <- dispersion_check("GWASQC_script.txt", plot=TRUE)
	text(Z$median_n, Z$mean_se, labels=Z$study, pos=c(2,4,2,1,2))

	
	
    

GWAtoolbox documentation built on May 2, 2019, 4:54 p.m.