Skip to contents


This document is a quick introduction to basic R. Audience would be users who are not familiar with R.

R syntax

  • Dot “.” is valid in a variable name or a function (e.g. variable element.subset, function ModelArray.lm())
  • Syntax for formula: Below is an example formula:
formula <- FD ~ age + sex

As you can see even though we did not define variable “FD”,“age” or “sex”, it’s a valid formula. Left hand side of “~” is dependent variable (y, or response), and right hand side includes the independent variables / covariates.

Prepare the phenotypes data.frame: manipulations

You may want to manipulate the data.frame phenotypes before passing it to ModelArray.lm() etc functions for model fitting. Examples like de-mean and rescale covariates. R package dplyr is useful and easy to use for manipulation.

# install is first via: install.packages("dplyr")
library(dplyr)    # load into memory
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>     filter, lag
#> The following objects are masked from 'package:base':
#>     intersect, setdiff, setequal, union