LMS Bioinformatics
April 2022
Links to material and slides for this course can be found on github - Reproducible-R
Or can be downloaded as a zip archive from here - Download zip
Once the zip file in unarchived. All presentations as HTML slides and pages, their R code and HTML practical sheets will be available in the directories underneath.
Before running any of the code in the practicals or slides we need to set the working directory to the folder we unarchived.
You may navigate to the unarchived Reproducible-R folder in the Rstudio menu
Session -> Set Working Directory -> Choose Directory
or in the console.
What is R?
R is a scripting language and environment for statistical computing.
Developed by Robert Gentleman and Ross Ihaka.
Inheriting much from S (Bell labs).
R comes with excellent “out-of-the-box” statistical and plotting capabilities.
R provides access to 1000s of packages (CRAN/MRAN/R-forge) which extend the basic functionality of R while maintaining high quality documentation.
In particular, Robert Gentleman developed the Bioconductor project where 100’s of packages are directly related to computational biology and analysis of associated high-throughput experiments.
Freely available from R-project website.
RStudio provides an integrated development environment (IDE) which is freely available from RStudio site
We will be using RStudio and R already installed on your machines.
The sqrt(25) demonstrates the use of functions in R. A function performs a complex operation on it’s arguments and returns the result.
In R, arguments are provided to a function within the parenthesis – ( ) – that follows the function name. So sqrt(ARGUMENT) will provide the square root of the value of ARGUMENT.
Other examples of functions include min(), sum(), max().
Note multiple arguments are separated by a comma.
## [1] 2## [1] 12## [1] 6R has many useful functions “built in” and ready to use as soon as R is loaded.
An incomplete, illustrative list can be seen here
In addition to R standard functions, additional functionality can be loaded into R using libraries. These include specialised tools for areas such as sequence alignment, read counting etc.
If you need to see how a function works try ? in front of the function name.
With functions such as min() and sqrt(), the arguments to be provided are obvious and the order of these arguments doesnt matter.
## [1] 4## [1] 4Many functions however have an order to their arguments. Try and look at the arguments for the dir() function using ?dir.
?dirOften we know the names of arguments but not necessarily their order. In cases where we want to be sure we specify the right argument, we provide names for the arguments used.
This also means we don’t have to copy out all the defaults for arguments preceeding it.
As with other programming languages and even graphical calculators, R makes use of variables.
A variable stores a value as a letter or word.
In R, we make use of the assignment operator <-
Now x holds the value of 10
## [1] 10## [1] 10Variables can be altered in place
## [1] 20Variables can be used just as the values they contain.
## [1] 25Variables can be used to create new variables
## [1] 25In R the most basic variable or data type is a vector. A vector is an ordered collection of values. The x and y variables we have previously assigned are examples of a vector of length 1.
## [1] 20## [1] 1To create a multiple value vector we use the function c() to combine the supplied arguments into one vector.
## [1] 1 2 3 4 5 6 7 8 9 10## [1] 10Vectors of continuous stretches of values can be created by the shortcut - :
## [1] 6 7 8 9 10Other useful function to create stretchs of numeric vectors are seq() and rep(). The seq() function creates a sequence of numeric values from a specified start and end value, incrementing by a user defined amount. The rep() function repeats a variable a user-defined number of times.
## [1] 1 3 5## [1] 1 5 10 1 5 10 1 5 10Square brackets [] identify the position within a vector (the index). These indices can be used to extract relevant values from vectors.
## [1] 1 2 3 4 5 6 7 8 9 10## [1] 1## [1] 8Indices can be used to extract values from multiple positions within a vector.
## [1] 1 6Negative indices can be used to extract all positions except that specified
## [1] 1 2 3 4 6 7 8 9 10We can use indices to modify a specific position in a vector
## [1] 1 2 3 4 5 6 7 8 9 10## [1] 1 2 3 4 -5 6 7 8 9 10Indices can be specified using other vectors.
## [1] 6 7 8 9 10## [1] 1 2 3 4 -5 0 0 0 0 0Remember!
Square brackets [] for indexing
## [1] 1Parentheses () for function argments.
## [1] 2Vectors in R can be used in arithmetic operations as seen with variables earlier. When a standard arithmetic operation is applied to vector, the operation is applied to each position in a vector.
## [1] 1 2 3 4 5 6 7 8 9 10## [1] 2 4 6 8 10 12 14 16 18 20Multiple vectors can be used within arithmetic operations.
## [1] 3 6 9 12 15 18 21 24 27 30So far we have only looked at numeric vectors or variables.
In R we can also create character vectors again using c() function. These vectors can be indexed just the same.
## [1] "CommonWealth"Character vectors can be used to assign names to other vectors.
## ICTEM CommonWealth Wolfson
## 1 2 3 These named vectors maybe indexed by a position's "name".## ICTEM Wolfson
## 1 3Index names missing from vectors will return special value “NA”
## <NA>
## NAA note on NA values
In R, like many languages, when a value in a variable is missing, the value is assigned a NA value.
Similarly, when a calculation can not be perfomed, R will input a NaN value.
NA values allow for R to handle missing data correctly but requires different handling than standard numeric or character values. We will illustrate an example handling NA values later.
The unique() function can be used to retrieve all unique values from a vector.
## [1] "Gene1" "Gene2" "Gene3" "Gene4" "Gene5"Logical vectors are a class of vector made up of TRUE/T or FALSE/F boolean values.
## [1] TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSELogical vectors can be used like an index to specify postions in a vector. TRUE values will return the corresponding position in the vector being indexed.
## [1] 1 3 5 7 9A common task in R is to subset one vector by the values in another vector.
The %in% operator in the context A %in% B creates a logical vector of whether values in A matches any values in of B.
This can be then used to subset the values within one character vector by a those in a second.
geneList <- c("Gene1","Gene2","Gene3","Gene4","Gene5","Gene1","Gene3")
secondGeneList <- c("Gene5","Gene3")
logical_index <- geneList %in% secondGeneList
logical_index## [1] FALSE FALSE TRUE FALSE TRUE FALSE TRUE## [1] "Gene3" "Gene5" "Gene3"Vectors may be evaluated to produce logical vectors. This can be very useful when using a logical to index.
Common examples are:
## [1] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE## [1] 6 7 8 9 10Logical vectors can be used in combination in order to index vectors. To combine logical vectors we can use some common R operators.
## [1] TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE## [1] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUESuch combinations can allow for complex selection of a vector’s values.
## [1] 1 2 3 4 5 6 7 8 9 10## [1] 5 6## [1] 7 8 9 10Exercise on vectors can be found here
Answers can be found here here
R code for solutions can be found here here
In programs such as Excel, we are used to tables.
All progamming languages have a concept of a table. In R, the most basic table type is a matrix.
A matrix can be created using the matrix() function with the arguments of nrow and ncol specifying the number of rows and columns respectively.
## [,1] [,2]
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## [5,] 5 10## [,1] [,2] [,3] [,4] [,5]
## [1,] 1 3 5 7 9
## [2,] 2 4 6 8 10By default when creating a matrix using the matrix function, the values fill the matrix by columns. To fill a matrix by rows the byrow argument must be set to TRUE.
## [,1] [,2] [,3] [,4] [,5]
## [1,] 1 3 5 7 9
## [2,] 2 4 6 8 10## [,1] [,2] [,3] [,4] [,5]
## [1,] 1 2 3 4 5
## [2,] 6 7 8 9 10To find dimensions of a matrix, the dim() function will provide dimensions as the row then column number while nrow() and ncol() will return just row number and column number respectively.
## [1] 5 2## [1] 5## [1] 2A matrix can be created from multiple vectors or other matrices.
cbind() can be used to attach data to a matrix as columns.
## x y
## [1,] 1 11
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## [4,] 4 14
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## [10,] 10 20rbind() functions to bind to a matrix as rows.
## x y
## 1 11
## 2 12
## 3 13
## 4 14
## 5 15
## 6 16
## 7 17
## 8 18
## 9 19
## 10 20
## z 21 22When creating a matrix using cbind() or matrix() from incompatable vectors then the shorter vector is recycled.
## Warning in matrix(1:5, ncol = 2, nrow = 3): data length [5] is not a sub-
## multiple or multiple of the number of rows [3]## [,1] [,2]
## [1,] 1 4
## [2,] 2 5
## [3,] 3 1For rbind() function, the longer vector is clipped.
## Warning in rbind(recycledMatrix2, c(1:5)): number of columns of result is not a
## multiple of vector length (arg 2)## [,1] [,2]
## [1,] 1 4
## [2,] 2 5
## [3,] 3 1
## [4,] 1 2As we have seen with vectors, matrices can be named. For matrices the naming is done by columns and rows using colnames() and rownames() functions.
namedMatrix <- matrix(1:10,ncol=5,nrow=2)
colnames(namedMatrix) <- paste("Column",1:5,sep="_")
rownames(namedMatrix) <- paste("Row",1:2,sep="_")
namedMatrix## Column_1 Column_2 Column_3 Column_4 Column_5
## Row_1 1 3 5 7 9
## Row_2 2 4 6 8 10Information on matrix names can also be retreived using the same functions.
## [1] "Column_1" "Column_2" "Column_3" "Column_4" "Column_5"## [1] "Row_1" "Row_2"Selecting and replacing portions of a matrix can be done by indexing using square brackets [] much like for vectors.
When indexing matrices, two values may be provided within the square brackets separated by a comma to retrieve information on a matrix position.
The first value(s) corresponds to row(s) and the second to column(s).
## [,1] [,2]
## [1,] 1 6
## [2,] 2 7
## [3,] 3 8
## [4,] 4 9
## [5,] 5 10Value of first column, second row
## [1] 2Similarly, whole rows or columns can be extracted. Single rows and columns will return a vector. When multiple columns or row indices are specified, a matrix is returned.
Values of second column (row index is empty!)
## [1] 6 7 8 9 10Values of third row (column index is empty!)
## [1] 3 8Values of second and third row (column index is empty!)
## [,1] [,2]
## [1,] 2 7
## [2,] 3 8As with vectors, names can be used for indexing when present
colnames(narrowMatrix) <- paste("Column",1:2,sep="_")
rownames(narrowMatrix) <- paste("Row",1:5,sep="_")
narrowMatrix[,"Column_1"]## Row_1 Row_2 Row_3 Row_4 Row_5
## 1 2 3 4 5## Column_1 Column_2
## 1 6## [1] 1As with vectors, matrices can be subset by logical vectors
## Column_1 Column_2
## Row_1 1 6
## Row_2 2 7
## Row_3 3 8
## Row_4 4 9
## Row_5 5 10## Row_1 Row_2 Row_3 Row_4 Row_5
## 1 2 3 4 5## Row_1 Row_2 Row_3 Row_4 Row_5
## TRUE TRUE TRUE TRUE FALSE## Column_1 Column_2
## Row_1 1 6
## Row_2 2 7
## Row_3 3 8
## Row_4 4 9As with vectors, matrices can have arithmetic operations applied to cells,rows, columns or the whole matrix
## Column_1 Column_2
## Row_1 1 6
## Row_2 2 7
## Row_3 3 8
## Row_4 4 9
## Row_5 5 10## [1] 3## Column_1 Column_2
## 3 8## [1] 5.5As with vectors, matrices can have their elements replaced
## Column_1 Column_2
## Row_1 1 6
## Row_2 2 7
## Row_3 3 8
## Row_4 4 9
## Row_5 5 10## Column_1 Column_2
## Row_1 10 1
## Row_2 2 1
## Row_3 3 1
## Row_4 4 1
## Row_5 5 1Matrices must be all one type (i.e. numeric or character).
Here replacing one value with character will turn numeric matrix to character matrix.
## Row_1 Row_2 Row_3 Row_4 Row_5
## 2 2 2 2 2## Column_1 Column_2
## Row_1 "Not_A_Number" "1"
## Row_2 "2" "1"
## Row_3 "3" "1"
## Row_4 "4" "1"
## Row_5 "5" "1"## Error in narrowMatrix[, 2] * 2: non-numeric argument to binary operatorExercise on matrices can be found here
Answers can be found here here
R code for solutions can be found here
A special case of a vector is a factor.
Factors are used to store data which may be grouped in categories (categorical data). Specifying data as categorical allows R to properly handle the data and make use of functions specific to categorical data.
To create a factor from a vector we use the factor() function. Note that the factor now has an additional component called “levels” which identifies all categories within the vector.
vectorExample <- c("male","female","female","female")
factorExample <- factor(vectorExample)
factorExample## [1] male female female female
## Levels: female male## [1] "female" "male"An example of the use of levels can be seen from applying the summary() function to the vector and factor examples
## Length Class Mode
## 4 character character## female male
## 3 1In our factor example, the levels have been displayed in an alphabetical order. To adjust the display order of levels in a factor, we can supply the desired display order to levels argument in the factor() function call.
## [1] male female female female
## Levels: male female## male female
## 1 3In some cases there is no natural order to the categories such that one category is greater than the other (nominal data). In this case we can see that R is gender neutral.
factorExample <- factor(vectorExample,levels=c("male","female"))
factorExample[1] < factorExample[2]## Warning in Ops.factor(factorExample[1], factorExample[2]): '<' not meaningful
## for factors## [1] NAIn other cases there will be a natural ordering to the categories (ordinal data). A factor can be specified to be ordered using the ordered argument in combination with specified levels argument.
factorExample <- factor(c("small","big","big","small"),ordered=TRUE,levels=c("small","big"))
factorExample## [1] small big big small
## Levels: small < big## [1] TRUEUnlike vectors, replacing elements within a factor isn’t so easy. While replacing one element with an established level is possible, replacing with a novel element will result in a warning.
## [1] big big big small
## Levels: big small## Warning in `[<-.factor`(`*tmp*`, 1, value = "huge"): invalid factor level, NA
## generated## [1] <NA> big big small
## Levels: big smallTo add a new level we can use the levels argument.
## [1] huge big big small
## Levels: big small hugeWe saw that with matrices you can only have one type of data. We tried to create a matrix with a character element and the entire matrix became a character.
In practice, we would want to have a table which is a mixture of types (e.g a table with sample names (character), sample type (factor) and survival time (numeric))
In R, we make use of the data frame object which allows us to store tables with columns of different data types. To create a data frame we can simply use the data.frame() function.
patientName <- c("patient1","patient2","patient3","patient4")
patientType <- factor(rep(c("male","female"),2))
survivalTime <- c(1,30,2,20)
dfExample <- data.frame(Name=patientName, Type=patientType,Survival_Time=survivalTime)
dfExample## Name Type Survival_Time
## 1 patient1 male 1
## 2 patient2 female 30
## 3 patient3 male 2
## 4 patient4 female 20Data frames may be indexed just as matrices.
## Name Type Survival_Time
## 1 patient1 male 1
## 2 patient2 female 30
## 3 patient3 male 2
## 4 patient4 female 20## Name Type Survival_Time
## 2 patient2 female 30
## 4 patient4 female 20Unlike matrices, it is possible to index a column by using the $ symbol.
dfExample <- data.frame(Name=patientName,Type=patientType,Survival_Time=survivalTime)
dfExample$Survival_Time## [1] 1 30 2 20## Name Type Survival_Time
## 1 patient1 male 1
## 3 patient3 male 2Using the $ allows for R to autocomplete your selection and so can speed up coding.
## [1] 1 30 2 20But this will not work..
The $ operator also allows for the creation of new columns for a data frame on the fly.
## Name Type Survival_Time
## 1 patient1 male 1
## 2 patient2 female 30
## 3 patient3 male 2
## 4 patient4 female 20## Name Type Survival_Time newColumn
## 1 patient1 male 1 newData
## 2 patient2 female 30 newData
## 3 patient3 male 2 newData
## 4 patient4 female 20 newDataCertain columns can not be replaced in data frames. Numeric columns may have their values replaced but columns with character values may not by default. This occurs because character vectors are treated as factors by default.
## Name Type Survival_Time newColumn
## 1 patient1 male 0 newData
## 2 patient2 female 30 newData
## 3 patient3 male 0 newData
## 4 patient4 female 20 newData## Name Type Survival_Time newColumn
## 1 patientX male 0 newData
## 2 patient2 female 30 newData
## 3 patientX male 0 newData
## 4 patient4 female 20 newDataIt is possible to update factors in data frames just as with standard factors.
dfExample <- data.frame(Name=patientName,Type=patientType,Survival_Time=survivalTime)
levels(dfExample[,"Name"]) <- c(levels(dfExample[,"Name"]) , "patientX")
dfExample[dfExample[,"Survival_Time"] < 10,"Name"] <- "patientX"
dfExample## Name Type Survival_Time
## 1 patientX male 1
## 2 patient2 female 30
## 3 patientX male 2
## 4 patient4 female 20If you wish to avoid using factors in data frames then the stringsAsFactors argument to data.frame() function should be set to FALSE
dfExample <- data.frame(Name=patientName,
Type=patientType,
Survival_Time=survivalTime,
stringsAsFactors = F)
dfExample[dfExample[,"Survival_Time"] < 10,"Name"] <- "patientX"
dfExample## Name Type Survival_Time
## 1 patientX male 1
## 2 patient2 female 30
## 3 patientX male 2
## 4 patient4 female 20A useful function in R is order()
For numeric vectors, order() by default returns the indices of a vector in that vector’s increasing order. This behaviour can be altered by using the “decreasing” argument passed to order.
## [1] 2 1 3## [1] 1 2 3## [1] 3 2 1When a vector contains NA values, these NA values will, by default, be placed last in ordering indices. This can be controlled by na.last argument.
## [1] 3 2 1 NA## [1] NA 3 2 1Since the order argument returns an index of intended order for a vector, we can use the order() function to order data frames by certain columns
## Name Type Survival_Time
## 1 patientX male 1
## 2 patient2 female 30
## 3 patientX male 2
## 4 patient4 female 20## Name Type Survival_Time
## 2 patient2 female 30
## 4 patient4 female 20
## 3 patientX male 2
## 1 patientX male 1We can also use order to arrange multiple columns in a data frame by providing multiple vectors to order() function. Ordering will be performed in order of arguments.
## Name Type Survival_Time
## 3 patientX male 2
## 1 patientX male 1
## 2 patient2 female 30
## 4 patient4 female 20A common operation is to join two data frames by a column of common values.
## Name Type Survival_Time
## 1 patient1 male 1
## 2 patient2 female 30
## 3 patient3 male 2
## 4 patient4 female 20## Name height
## 1 patient1 6.1
## 2 patient2 5.1
## 3 patient3 5.5To do this we can use the merge() function with the data frames as the first two arguments. We can then specify the columns to merge by with the by argument. To keep only data pertaining to values common to both data frames the all argument is set to TRUE.
## Name Type Survival_Time height
## 1 patient1 male 1 6.1
## 2 patient2 female 30 5.1
## 3 patient3 male 2 5.5Exercise on data frames can be found here
Answers can be found here here
R code solutions can be found here
Lists are the final data-type we will look at.
In R, lists provide a general container which may hold any data types of unequal lengths as part of its elements. To create a list we can simply use the list() function with arguments specifying the data we wish to include in the list.
firstElement <- c(1,2,3,4)
secondElement <- matrix(1:10,nrow=2,ncol=5)
thirdElement <- data.frame(colOne=c(1,2,4,5),colTwo=c("One","Two","Three","Four"))
myList <- list(firstElement,secondElement,thirdElement)
myList## [[1]]
## [1] 1 2 3 4
##
## [[2]]
## [,1] [,2] [,3] [,4] [,5]
## [1,] 1 3 5 7 9
## [2,] 2 4 6 8 10
##
## [[3]]
## colOne colTwo
## 1 1 One
## 2 2 Two
## 3 4 Three
## 4 5 FourJust as with vectors, list elements can be assigned names.
## $First
## [1] 1 2 3 4
##
## $Second
## [,1] [,2] [,3] [,4] [,5]
## [1,] 1 3 5 7 9
## [2,] 2 4 6 8 10
##
## $Third
## colOne colTwo
## 1 1 One
## 2 2 Two
## 3 4 Three
## 4 5 FourList, as with other data types in R can be indexed. In contrast to other types, using [] on a list will subset the list to another list of selected indices. To retrieve an element from a list in R , two square brackets [[]] must be used.
## [[1]]
## [1] 1 2 3 4## [1] 1 2 3 4As with data.frames, the $ sign may be used to extract named elements from a list
## [1] 1 2 3 4Again, similar to vectors, lists can be joined together in R using the c() function
myNamedList <- list(First=firstElement,Second=secondElement,Third=thirdElement)
myNamedList <- c(myNamedList,list(fourth=c(4,4)))
myNamedList[c(1,4)]## $First
## [1] 1 2 3 4
##
## $fourth
## [1] 4 4Note that on last slide we are joining two lists. If we joined a vector to a list, all elements of the vector would become list elements.
## [[1]]
## [1] 1 2 3 4
##
## [[2]]
## [,1] [,2] [,3] [,4] [,5]
## [1,] 1 3 5 7 9
## [2,] 2 4 6 8 10
##
## [[3]]
## colOne colTwo
## 1 1 One
## 2 2 Two
## 3 4 Three
## 4 5 Four
##
## [[4]]
## [1] 4
##
## [[5]]
## [1] 4Sometimes you will wish to “flatten” out a list. When a list contains compatable objects, i.e. list of all one type, the unlist() function can be used. Note the maintenance of names with their additional sufficies.
## $First
## [1] 1 2 3
##
## $Second
## [1] 2 6 7
##
## $Third
## [1] 1 4 7## First1 First2 First3 Second1 Second2 Second3 Third1
## 1 2 3 2 6 7 1A common step is to turn a list of standard results into matrix. This can be done in a few steps in R.
myNamedList <- list(First=c(1,2,3),Second=c(2,6,7),Third=c(1,4,7))
flatList <- unlist(myNamedList)
listAsMat <- matrix(flatList,
nrow=length(myNamedList),
ncol=3,
byrow=T,
dimnames=list(names(myNamedList)))
listAsMat## [,1] [,2] [,3]
## First 1 2 3
## Second 2 6 7
## Third 1 4 7Most of the time, you will not be generating data in R but will be importing data from external files.
A standard format for this data is a table
| Gene_Name | Sample_1.hi | Sample_2.hi | Sample_3.hi | Sample_4.low | Sample_5.low | Sample_1.low |
|---|---|---|---|---|---|---|
| Gene_a | 2.874648 | 4.960330 | 4.241958 | 4.998319 | 3.331386 | 3.1546449 |
| Gene_b | 2.607975 | 3.470672 | 4.788898 | 4.081167 | 3.499954 | 3.4684829 |
| Gene_c | 4.494620 | 3.335393 | 3.934351 | 2.345385 | 3.834476 | 3.0744386 |
| Gene_d | 4.465812 | 4.068829 | 5.495932 | 9.872878 | 8.675069 | 8.3544254 |
| Gene_e | 9.429507 | 11.527502 | 9.862680 | 2.910204 | 3.799027 | 0.2920961 |
| Gene_f | 9.483906 | 10.616366 | 9.591775 | 2.168146 | 3.811851 | 0.9630530 |
| Gene_g | 8.482135 | 10.623470 | 9.158943 | 10.962945 | 10.923468 | 9.8027708 |
| Gene_h | 8.632512 | 9.396295 | 10.444425 | 8.719504 | 9.368551 | 9.8399054 |
Tables from text files can be read with read.table() function
## Gene_Name Sample_1.hi Sample_2.hi
## 1 Gene_a 4.111851 3.837018
## 2 Gene_b 6.047822 5.683518
## 3 Gene_c 2.597068 3.316300
## 4 Gene_d 6.009197 5.927419Here we have provided two arguments. - sep argument specifies how columns are separated in our text file. (“,” for .csv, " for .tsv) - header argument specifies whether columns have headers.
read.table() allows for significant control over reading files through its many arguments. Have a look at options by using ?read.table
The row.names argument can be used to specify a column to use as row names for the resulting data frame. Here we use the first column as row names.
## Sample_1.hi Sample_2.hi Sample_3.hi
## Gene_a 4.111851 3.837018 4.360628
## Gene_b 6.047822 5.683518 4.315889
## Gene_c 2.597068 3.316300 3.681509
## Gene_d 6.009197 5.927419 2.244701As mentioned, data which is read into R through read.table() will be of data frame class.
To avoid character columns being converted into factors, we can specify the stringsAsFactors argument here.
Other very useful functions for read table include: - skip - To set number of lines to skip when reading. - comment.char - To set the start identifier for lines not to be read.
The read.table function can also read data from http.
URL <- "http://mrccsc.github.io/readThisTable.csv"
Table <- read.table(URL,sep=",",header=T)
Table[1:2,1:3]## Gene_Name Sample_1.hi Sample_2.hi
## 1 Gene_a 4.111851 3.837018
## 2 Gene_b 6.047822 5.683518And the clipboard.(This is Windows version)
read.table() function will by default read every row and column of a file.
The scan() function allows for the selection of particular columns to be read into R and so can save memory when files are large.
## [[1]]
## [1] "Gene_a" "Gene_b" "Gene_c" "Gene_d" "Gene_e" "Gene_f" "Gene_g" "Gene_h"
##
## [[2]]
## NULL
##
## [[3]]
## NULLOnce we have our data analysed in R, we will want to export it to a file.
The most common method is to use the write.table() function
Since our data has column names but no row names, I will provide the arguments col.names and row.names to write.table()
Exercise on reading and writing data can be found here
Answers can be found here
R code for solutions can be found here
R libraries or packages are collections of functions developed by the community. R packages include - reusable R functions - the documentation for these functions and - sample data to test their functionality.
A repository is a place where packages are deposited by the community and you can install them from it. The two most popular repositories for R packages are: - CRAN - Bioconductor
You can install the packages from CRAN using the function install.packages()
For example,
To load the installed packages and use them, you can use the library() function
For example,
You can also install packages through the R studio menu
-> Tools -> Install packages ..
To install packages from Bioconductor, you have to first have to install the Bioconduction package manager “BiocManager”
To install it,
Then, you can install any packages from Bioconductor using the BiocManager::install() function
For example,
To load the installed packages and use them, you can use the library() function
For example,
If you are using an older version of R (R < 3.5.0), you have to use biocLite to install Bioconductor packages.
To install packages from Bioconductor, you have to first source the “biocLite” package.
Then, you can install any packages from Bioconductor using the biocLite() function
For example,
To load the installed packages and use them, you can use the library() function
For example,
You can get the documentation of the package by using the function help() or “??”
For example
For a more detailed information on each and every parameter of all the functions in a package, you can refer to the reference manual or the in the package webpage or by using the browseVignettes() function.
For example,
You can see what libraries are available in the Packages panel or by the library() function with no arguments supplied
End of Session 1
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