This site makes available the results from a phenotype association study using lowpass whole genome sequencing from 962 individuals from the CHARGE consortium. The data, and a userfriendly interface, are available in the form of an R package which makes use of R's powerful plotting capabilities. A more detailed description of the study design and analyses are available in:
Wholegenome sequence–based analysis of highdensity lipoprotein cholesterol
Description of the R Package: lachesis is an R package which which coordinates the display of summary statistics from a suite of genotypephenotype analyses, which we illustrate with an analysis of HDL cholesterol. The package takes as input either a gene name or a range of positions (in hg19 coordinates) and returns summary statistics for the analyses in that region, which can be plotted or viewed as a table. The package is available here: Lachesis Download page
Documentation for the package is contained in R, which can be accessed for the two main functions with the commands:
Some illustrative examples of the package capabilities can be seen with the command:
Installation instructions:
The package can be installed in R on Windows, Mac OSX, or Linux via the command
where "/path_to_directory/" specifies where you have downloaded the file.
If you do not have R, you can find the latest version and installation instructions here: http://www.rproject.org/
Description of the available data:
For any particular region, the following tables of summary statistics are available, and returned when queried using the R package. Each statistic was adjusted for age, sex, BMI and cohort.
oreg
