R Data Skills for Bioinformatics: Glossary

Use RStudio to create and manage projects with consistent layout.

Treat raw data as read-only.

Treat generated output as disposable.

Separate function definition and application.

Use version control.

R has the usual arithmetic operators and mathematical functions.

Use <- to assign values to variables.

Use ls() to list the variables in a program.

Use rm() to delete objects in a program.

Use install.packages() to install packages (libraries).

Use library(packagename)to make a package available for use

Use help() to get online help in R.

Atomic vectors are usually created with c(), short for combine;

Lists are constructed by using list();

Data frames are created with data.frame(), which takes named vectors as input;

The basic data types in R are double, integer, complex, logical, and character;

All objects can have arbitrary additional attributes, used to store metadata about the object;

Adding a dim() attribute to an atomic vector creates a multi-dimensional array;

Access individual values by location using [].

Access slices of data using [low:high].

Access arbitrary sets of data using [c(...)].

Use which to select subsets of data based on value.

Read in a csv file using read_csv()

View a dataframe with View

Use filter() to pick observations by their values

Use arrange() to order the rows

Use select() to pick variables by their names

Use mutate() to create new variables with functions of existing variables

Use summarize() to collapse many values down to a single summary

Use ggplot2 to create plots.

Think about graphics in layers: aesthetics, geometry, statistics, scale transformation, and grouping.

Use function to define a new function in R.

Use parameters to pass values into functions.

Load functions into programs using source.

Use if and else to make choices.

Use for to repeat operations.

Use read_cvs to read in CSV files

Use read_tvs to read in TSV files

Use write_csv() and write_tsv() to write such files

Supply col_types to read functions in your script to insure consistancy

Use guess_encoding() to guess encoding of strings in old docs