V3

Question 1

data from R packages

Answer 1

• can be loaded with the data() function

- example : data (USArrests)

Question 2

how to load a small part of data set (code)

Answer 2

• head(dataset)

Question 3

read data (code)

Answer 3

• read.table() and read.csv()

my data

Question 4

row.names()

Answer 4

a vector containing the row names

a single number giving the column of the table which contains the row names

Question 5

col.names()

Answer 5

a vector giving the column names

Question 6

check.names()

Answer 6

names of the variables in the data frame are checked to ensure that they are syntactically valid variable names

Question 7

skip()

Answer 7

the number of lines of the data file to skip before beginning to read data

Question 8

how to define what classes we expect in the different colums (code)

Answer 8

• numerical, logical, factor, character

- colClasses = c(“Character”, “factor”, …)

Question 9

how to get dimension of table (code)

Answer 9

dim()

Question 10

load in text files on a line by kine basis, why and (code)

Answer 10

readLines(“my text.txt”, n = 10) - read first 10 lines
readLines(“my text.txt”, n = -1) - read everything
- for big amounts of row wise data , data might be to big to load at once

Question 11

function to read zip file

Answer 11

gzfile(“data.gz”, “r”) - “r” for read (w for write)

Question 12

how to use url as a connection

Answer 12

url()

Question 13

how to read excel file

Answer 13

• no native suport for xlsx in R
• available in libraries : xlsx - use4 java to read and write xlsx files
• slow and unreliable
• just export xlsx files as csv

Question 14

loading binary files

Answer 14

readBin()
- 2 dimensional array of pixels
- each pixel defined by 3 busted (B, G, R)
readBin, before remove header
image

Question 15

%in%

Answer 15

• allows you to filer A %in% B
• which columns of matrix A in matrix B
  AinB

Question 16

which function

Answer 16

transforms a logical vector into a numeric one (by index)

before TRUE, FALSE, TRUE, TRUE, FALSE
code : which (AinB)
after: 1, 3 ,4

Question 17

subset()

Answer 17

• creates a subset

subset(air quality, Temp > 80, select = c(Ozone, Temp))

Question 18

saving data

Answer 18

write.table(data, file=”data.txt”, sep”\t”, row.names = FALSE)

Question 19

biomaRt

Answer 19

• a community-driven project to provide unified access to distributed research data to facilitate the scientific discovery process
• most of not all biological relevant databases

Question 20

important concepts in biomaRt

Answer 20

mart - link to a database : ListMarts()
attributes - what do we want to retrieve: ListAttributes()
filters - what do our values mean : ListFilters()