R Code Module 1

Data frames

The most important data structure for data analysis in R within the file 1B

Rows

Observations such as samples or experiments

Columns

Variables such as measurements or categories

Mixed data types

A property of data frames where each column can contain different types of data

data.frame()

A function used to combine vectors into a new data frame

cbind()

A function used to combine or add columns to a data frame

rbind()

A function used to combine or add rows to a data frame

str()

A function used to check the structure and data types of a data frame

dim()

A function that returns the dimensions, specifically the rows and columns, of a data frame

nrow()

A function that returns the number of rows in a data frame

ncol()

A function that returns the number of columns in a data frame

colnames()

A function used to check or rename the column names of a data frame

rownames()

A function that returns the row names of a data frame, which are usually numbers

$

An operator used to access elements or add new columns by their specific name

[row, column]

An operator used to access data frame elements by their position

[condition, ]

An indexing format used with logical conditions to filter and access specific rows

subset()

A function that provides cleaner syntax to filter data frames based on conditions and create subsets

which()

A function used to find row positions based on a specific condition

ifelse()

A function used to add categorical columns or generate conditional values

NULL

A value assigned to a column to remove it completely from a data frame

names()

A function used to rename columns

order()

A function used to get sorting indices in order to sort data frames by single or multiple columns

decreasing = TRUE

An argument used within sorting functions to specify descending order

head()

A function used to preview the first few rows of a data frame

tail()

A function used to preview the last few rows of a data frame

which.min()

A function used to find the row containing the minimum value

which.max()

A function used to find the row containing the maximum value

summary()

A function used to obtain comprehensive statistical summaries for data frame columns

table()

A function used to count categorical data or perform cross

sapply()

A function used to apply functions across multiple numeric columns simultaneously

aggregate()

A function used to calculate summary statistics, such as the mean, by a specific group

save.image()

A function used to save the R workspace to preserve all created objects

is.na()

A function used to check for missing values within a data frame or column

na.rm

An argument used within functions (such as mean or sd) to specify whether missing values should be removed or ignored prior to calculation

Vector

The most fundamental data structure in R that stores a sequence of elements of the same type, such as numeric, character, or logical elements

1

based indexing

c()

A function used to combine individual values and different types into a vector

seq()

A function used to create sequences of numbers with specific patterns, steps, or lengths

rep()

A function used to repeat specific values or a sequence

:

An operator used to generate simple integer sequences

Quotes ("")

Formatting used to define character values

TRUE/FALSE

Keywords used to define logical values

>

A comparison operator used to create logical vectors

*

An arithmetic operator used for element

log()

A function that calculates the natural logarithm of each value in a vector

length()

A summary function that counts the total number of elements present in a vector

sum()

A summary function that calculates the total sum of all values in a vector

mean()

A summary function that calculates the average value of a vector

median()

A summary function that determines the median value of a vector

sd()

A summary function that calculates the standard deviation of a vector

sort()

A function used to arrange values in ascending order, or descending order when using the decreasing = TRUE parameter

unique()

A function used to remove duplicates and find distinct values within a vector

which()

A function used to find the index positions of elements that meet a specific logical condition

rev()

A function used to reverse the order of elements in a vector

prod()

A function used to calculate the product of all values in a vector

which.max()

A function used to find the specific index position of the maximum value in a vector

[position]

Indexing syntax used to access a specific vector element by its numerical position

[c(positions)]

Indexing syntax used to access multiple vector elements at once by passing specific positions

[logical_vector] or [condition]

Indexing syntax used to subset and access vector elements based on a logical condition

[-position]

Indexing syntax that uses negative indexing to exclude specific elements from a vector

read.csv()

Function used to import CSV (comma

read.table()

Function used to import files with custom delimiters

read.delim()

Function used to import tab

write.csv()

Function used to export data to a CSV file

write.table()

Function used to export data to a file with custom separators, such as tabs

Working directory

The folder R looks for files in

File paths

How to specify file locations

Data validation

Checking imported data for issues

Encoding

How text is stored in files

CSV files

Comma

TSV files

Tab

TXT files

Space or other delimited files

getwd()

Function to see the current working directory

setwd()

Function to change the working directory

list.files()

Function to list available files and folders in a directory

file.exists()

Function to check if specific files exist

file.info()

Function to get file information like size and modification date

dir.create()

Function to create a new directory

header = TRUE

Option specifying that the first row of a file contains column names

stringsAsFactors = FALSE

Option to keep text columns as characters instead of converting them to factors

na.strings

Option used to specify missing value indicators, such as empty strings or "N/A"

dim()

Function to check the dimensions of a data frame

str()

Function to check data types and structure

sep

Parameter used to specify the delimiter (e.g., "\t") in read and write functions

save.image()

Function used to save the workspace to preserve all created object

Descriptive statistics

Statistics used to summarize data, including mean, median, and standard deviation

Inferential statistics

Statistics used to make conclusions about populations, such as t

mean()

Calculates the central tendency or basic average of data

median()

Calculates the median value for basic statistics

sd()

Calculates the standard deviation to measure data spread

summary()

Provides a comprehensive overview of descriptive statistics

quantile()

Calculates specific percentiles and quartiles from the data

range()

Finds the minimum and maximum values to show data spread

min()

Finds the extreme minimum value in the data

max()

Finds the extreme maximum value in the data

IQR()

Calculates the interquartile range to measure data spread

data.frame()

Creates a summary table to combine and organize calculated statistics

sapply()

Applies functions to multiple columns, often used with is.numeric to identify numeric columns

aggregate()

Calculates statistics grouped by specific variables