Introduc)onto

BISTBiosta+s+cscourseMay6th,2016SarahBonnin

CRGBioinforma)csCoreFacility

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Outline

•  R:what,when,why?•  GeEngstarted•  Datastructures•  Libraries/Packages•  Basiccommands•  Func)ons•  RStudio

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R:what,when,why?

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WhatisR?

•  IntegratedsuiteofsoNwarefacili)esfordatamanipula+on,calcula+onandgraphicaldisplay.

•  Simpleandeffec)veprogramminglanguagewhichincludescondi)onals,loopsetc.

•  Implementa)onoftheSprogramminglanguage(Belllaboratories)

R:what,when,why?

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WhatisR?

•  CreatedbyRossIhakaandRobertGentlemanattheUniversityofAuckland,NewZealand

•  Nowdevelopedbythe“Rdevelopmentcoreteam”

•  GNUproject(freesoNware,passcollabora)on)

àOpensource!

R:what,when,why?

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h]ps://www.r-project.org/

R:what,when,why?

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WhentouseR?

•  Dataanalysis•  Sta)s)calmodeling•  Simula)on•  Graphics

R:what,when,why?

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WhytouseR?

•  Flexible•  Powerful•  Interac)ve•  Veryac+vecommunityofdevelopersandusers!

R:what,when,why?

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R:what,when,why?

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GeDngstarted

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Rsyntax

func+on(arguments)example:

list.files(path=".")

command argument

Ge.ngstarted

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Rsyntax

a<-func+on(arguments)example:

myobject<-list.files(path=".")

object assignmentoperator

Ge.ngstarted

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Rsyntax

•  Casesensi)ve:List.fileslist.files

•  Commentlinesstartwith#

•  Commandsseparatedby;oranewline

•  Argumentsinafunc)onseparatedby,

Ge.ngstarted

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GeEnghelp

•  help(func+on)•  ?func+on

•  Google!

Ge.ngstarted

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Star)ngRinterac)velyfromaterminal

•  Star)ngsession:R•  Endingsession:q()

Ge.ngstarted

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DataStructures

Vectors

Factors

Matrices

Dataframes

List

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DataTypes•  Everyvaluehasadatatypethattellswhatsortofvalueitis.

•  Mostcommondatatypes:

–  Numeric(Numbers)–  Character(Text)–  Logical(True/False)

•  Checkingobjecttypewithmode():–  mode("a")/[1]"character”–  mode(10)/[1]"numeric”–  mode(FALSE)/[1]"logical"

Datastructures

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Vectors

•  Sequenceofdataelementsofthesametype•  Elementsofanatomicvectorareofonetypeonly,either:– Numeric(1,2,5.3,6,-2,4)– Character("one","two","three")– Logical(TRUE,TRUE,TRUE,FALSE,TRUE,FALSE)

Datastructures

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Vectors

•  Assignmentofvaluestovectorusingtheccommand(combiningelements)

myvector<-c(0.5,2,10,3,8)myvector<-1:5•  Checkingifanobjectisavectorwithis.vector(myvector)

Datastructures

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sameasc(1,2,3,4,5)

Vectors

•  Fetchelementsofavector:subscripts

a

a[1]a[2:4]a[c(5,7)]

1 9 4 8 0 11 7

Datastructures

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Factors

•  Vectorobjectusedtospecifyadiscreteclassifica+onofthecomponentsinadataset:

àCategoricalvariables

•  Usedmainlyinsta+s+calmodeling,butalsoinsomegraphicalfunc)ons.

•  Similartovectors,buttheirvaluesarelimitedtoafixedsetofpossiblevalues.

Datastructures

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Factors

•  Bothnumericandcharactervariablescanbemadeintofactors.

myfactor<-factor(c("a","a","b","c",1,2))

myfactor[1]aabc12Levels:12abc

Datastructures

Levelsarecharactervectors

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Factors

•  Checkingifanobjectisafactor:–  is.factor(myfactor)

•  Transformingavectorintoafactor:– as.factor(myvector)

Datastructures

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Matrices

•  Amatrixisavectorof2dimensions•  Allcolumnsinamatrixmusthave:–  thesametype(numeric,character,logical)–  thesamelength

a<-matrix(c(1,0,34,5,13,44,12,4,3,8,6,9,22,7,76),

nrow=5, ncol=3)

Datastructures

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Matrices

•  Fetchrows,columnsorsingleelementsofamatrixusingsubscript:

a[,]

Datastructures

rowindices

columnindices

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Matrices

•  Fetchrows,columnsorsingleelementsofamatrixusingsubscript:

a1 44 6

0 12 9

34 4 22

5 3 7

13 8 76

a[1,]

a[2:3,]

a[,3]

a[5,1]

Datastructures

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Dataframes

•  Structuresof2dimensions.

•  Moregeneralthanmatrices.•  Differentcolumnscanhavedifferenttypesbutmusthavethesamelength.

a<-data.frame(c(1,3,34,5,13),

c(“etc”,“ok”,“yes”,“no”,“well”), c(TRUE,TRUE,FALSE,FALSE,TRUE))

Datastructures

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1 etc TRUE

3 ok TRUE

34 yes FALSE

5 not FALSE

13 well TRUE

Dataframes

•  Fetchrows,columnsorsingleelementsofadataframeusingsubscript:

a

a[1,]

a[2:3,]

a[,3]

a[5,1]

Datastructures

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Matricesanddataframesdimensionnames

a<-matrix(c(1,0,34,5,13,44), nrow=3, ncol=2, dimnames=list(c(”row1”,”row2”,”row3”),c(”col1”,”col2”)))

b<-data.frame(c(1,0,34),

c(5,13), row.names=c("row1","row2","row3"), col.names=,c(”col1”,”col2”))

Datastructures

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Matricesanddataframesdimensionnames

•  Changingcolumnand/orrownames:colnames(x)<-c(“a”,“b”,“c”)rownames(x)<-1:5

•  Changingcolumnandrownamesatonce:dimnames(x)<-list(c(“a”,“b”,“c”),1:5)

Datastructures

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Matricesanddataframesdimensionnames

col1 col2

row1 1 5

row2 0 13

row3 34 44

Matrix Dataframe

a[,"col1”]

a["col1”]

a$col1

a["row1",]

a["row1”]

a["row1","col1"]

b[,"col1”]

b["col1”]

b$col1

b["row1",]

b["row1”]

b["row1","col1"]

Datastructures

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MatricesanddataframesChecksandconversions

Datastructures

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•  Checkingiftheobjectisamatrix…is.matrix(mymatrix)

…oradataframe:is.data.frame(mydataframe)

•  Conver)ngamatrixintoadataframe…as.matrix(mydataframe)

…orviceversa:as.data.frame(mymatrix)

Lists

•  Linearstructures.•  Acomponentofalistcanbeanydatastructure

(matrix,vector,dataframe,anotherlist)

Datastructures

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Lists

•  Createalist:x<-list()x<-list(c(“fir”,“sec”,“th”),

c(0,20,4,2), TRUE, matrix(c(2,5,4,6,3,7), nrow=2,ncol=3))

Datastructures

#1stelementofthelist

#2delementofthelist

#3delementofthelist

#4thelementofthelist

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#Emptylistthatcanbefilledlateron

Lists

•  Accessingelementsofalistx:

x[[1]]x[[2]][3]

x[[4]][1,2]

“fir”,“sec”,”th” 0,20,4,2 TRUE2 4 3

5 6 7

Datastructures

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Namingelementsofalist

x<-list(charvector=c(“fir”,“sec”,“th”), numvector=c(0,20,4,2), oneboolean=TRUE, onematrix=matrix(c(2,5,4,6,3,7), nrow=2,ncol=3))

ornames(x)<-c(“charvector”,“numvector”,“oneboolean”,“onematrix”)

Datastructures

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Accessingelementsoflistxpername

x[“charvector”]or

x$charvector

x[“numvector”][3]or

x$numvector[3] x[“onematrix”][1,2]or

x$onematrix[1,2]

“fir”,“sec”,”th” 0,20,4,2 TRUE2 4 3

5 6 7

charvector numvector oneboolean onematrix

Datastructures

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Lengthanddimensionoflists

•  Listshavealengthbutonlyonedimension

•  Elementswithinalistcanhavelengthsanddimensions,dependingontheirdatastructure.

Datastructures

“fir”,“sec”,”th” 0,20,4,2 TRUE2 4 3

5 6 7

length(x)

4

length(x[[2]])

4dim(x[[4]])

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Checkingandconver)ngdatatypesandstructures

Datastructures

Checking Conver+ngis.matrix(x) as.matrix()

is.data.frame(x) as.data.frame()

is.vector() as.vector()

is.list() as.list()

is.factor() as.factor()

is.character() as.character()

is.numeric() as.numeric()

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Library/packages

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Library/packages

•  Packagesarecollec)onsofRfunc)ons,data,andcompiledcodeinawell-definedformat.

•  Thedirectorywherepackagesarestorediscalledthelibrary.

Library/packages

Defini&onsfromh.p://www.statmethods.net/interface/packages.html06/05/16 41

Standardpackages

•  About25standardpackagesaresuppliedwithRbydefault(example:base,stats,graphics).

•  OnMay4th2016,8340packageswereavailable!•  AnyonecancontributetotheRpackagerepository

Library/packages

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Installingandloadingpackages

•  Packagescanbeinstalledfrom:

–  theinterac)vesession:install.packages(“ggplot2”)install.packages(“ggplot2”,repos=

h]p://cran.r-project.org/web/packages/)

–  theterminal:RCMDINSTALLggplot2_version.tar.gz

•  Andloaded:library(“ggplot2”)

Library/packages

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Lis)ngpackages

•  Installedpackages:library()acepackace()andavas()forselec)ngregressiontransforma)onsaffyMethodsforAffymetrixOligonucleo)deArraysaffyioToolsforparsingAffymetrixdatafilesAnnota)onDbiAnnota)onDatabaseInterfaceBiobaseBiobase:Basefunc)onsforBioconductorBiocGenericsS4genericfunc)onsforBioconductor…•  Loadedpackages:search()[1]".GlobalEnv""package:stats""package:graphics"[4]"package:grDevices""package:u)ls""package:datasets"[7]"package:methods""Autoloads""package:base"

Library/packages

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Lis)ngfunc)onsfrompackages

•  ls(“package:yourpackage”)•  ls(“package:VennDiagram”)[1]"add.)tle""adjust.venn"[3]"calculate.overlap""decide.special.case"[5]"draw.pairwise.venn""draw.quad.venn"[7]"draw.quintuple.venn""draw.single.venn"…."

Library/packages

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Accessingpackage’sfunc)ons

•  Usually,callingthefunc)onbyitsnameisenough:add.+tle()

•  If2packageshaveafunc)onwiththesamename,makesureyouareusingtherightone:VennDiagram::add.+tle()

Library/packages

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Basiccommands

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GeEngandchangingworkingdirectory

•  getwd()– Returnscurrentworkingdirectory

•  setwd(“/home/mydir/”)– Changescurrentworkingdirectoryto“/home/mydir”

Basiccommands

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Informa)onaboutobjects•  summary(x)

àfornumericaldata:min,max,medianetc.àforcharacterdata:countofitemsoccurrences

Basiccommands

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col1 col2 col3

1 ok TRUE

3 yes FALSE

5 no FALSE

6 maybe FALSE

col1col2col3Min.:1.00maybe:1Mode:logical1stQu.:2.50no:1FALSE:3Median:4.00ok:1TRUE:1Mean:3.75yes:1NA's:03rdQu.:5.25Max.:6.00

Informa)onaboutobjects

•  str(x):àInternalstructureofanRobject

'data.frame':4obs.of3variables:$col1:num1356$col2:Factorw/4levels"maybe","no","ok",..:3421$col3:logiTRUEFALSEFALSEFALSE

Basiccommands

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col1 col2 col3

1 ok TRUE

3 yes FALSE

5 no FALSE

6 maybe FALSE

Size/dimensionsofobjectsBasiccommands

numberofelementsinvector,factororlist length(x)

dimensionsofmatrixordataframe dim(x)

numberofrowsofmatrixordataframe nrow(x)

numberofcolumnsofmatrixordataframe ncol(x)

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Elementaryarithme)coperatorsBasiccommands

addi)on +

subtrac)on -

division /

mul)plica)on *

exponen)a)on ^or**

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LogicaloperatorsBasiccommands

inferior <inferiororequal <=

superior >superiororequal >=

equality ==inequality !=

intersec)on(“and”) &union(“or”) |

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Obtainingsummarysta)s)csBasiccommands

average/mean mean(x)

median median(x)

minimum min(x)

maximum max(x)

variance var(x)

correla)on cor(x)

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Somecommonarithme)cfunc)onsBasiccommands

naturallogarithm log(x)exponen)alfunc)on

e^x exp(x)

sine sin(x)

cosine cos(x)

tangent tan(x)

absolutevalue abs(x)

squareroot sqrt(x)

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Objectsstoredintheglobalenvironment

•  Lis)ng:ls()orobjects()•  Removingoneobjectfromenvironment:rm(x)•  Removingseveralobjects:rm(x,y)

•  Removingallobjectfromenvironment:rm(list=ls())

Basiccommands

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Readingandwri)ngfilesBasiccommands

Readingfileintoobject

a<-read.table(“file.txt”)

Wri)ngobjecttofile

write.table(a,“file.txt”)

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Savingobjectsorsession

•  Saveobjectsxandyinto“myobjects.RData”file– save(x,y,file=“myobjects.RData”)

•  Loadobjectsxandyintocurrentdirectory:–  load(“myobjects.RData”)

•  Savethecurrentworkspace(allobjects):– save.image(file=“.RData”)

Basiccommands

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Commandhistory

•  Last25commands:–  history()

•  Allpreviouscommands–  history(max.show=Inf)

•  Savecommandhistory:–  savehistory()

•  Loadcommandhistory:–  loadhistory()

Basiccommands

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Informa)onaboutthecurrentsession

sessionInfo()

Basiccommands

Rversion

PlavormandOSversion

Packagesawached

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Func+onsinR

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Knowingthesourcecodeofafunc)on

•  Nameofthefunc)onwithout()Forexample:

sort

func)on(x,decreasing=FALSE,...){if(!is.logical(decreasing)||length(decreasing)!=1L)stop("'decreasing'mustbealength-1logicalvector.\nDidyouintendtoset'par)al'?")UseMethod("sort")}

Func@ons

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User-wri]enfunc)ons

•  Func)onsarepiecesofcodewri]entocarryout(a)specifiedtask(s)andbeabletorepeatit(them)easily.

•  Rallowsyoutocreateyourownfunc)ons.

Func@ons

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Func)ons’structure

myfunc+on<-func+on(arg1,arg2,...){ commands return(something)}

Func@ons

Func+on’sname Crea+ngthefunc+on

myfunc+on’slistofarguments

whatmyfunc+ondoes

Value/objectmyfunc+onreturns

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Func@ons

Objectsinafunc+onarelocaltothatfunc+on!

fromhBps://www.datacamp.com/community/tutorials/func@ons-in-r-a-tutorial06/05/16 65

Objectsinfunc)onsmyfunc+on<-func+on(arg1){a<-arg1return(a+1)

}

Func@ons

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>a<-12>myfunc)on(10)[1]11>a[1]12

>myfunc)on(10)[1]11>aError:object'a'notfound

Exampleofafunc)on

Func+on“somestats”:

takesasanargument:onenumericvector.computes:medianandmeanofthatvector.returns:avectorcontainingthese2values.

Func@ons

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Exampleofafunc)onsomestats<-func)on(vector_input){ my_mean<-mean(vector_input) my_median<-median(vector_input)

return(c(my_mean,my_median))}

x<-c(0,2,1,6.3,2.2,10,8,5.4)

somestats(x)4.36253.8000

Func@ons

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Savingandsourcingfunc)onsFunc@ons

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somestats<-func)on(vector_input){ my_mean<-mean(vector_input) my_median<-median(vector_input) vector_output<-c(my_mean,my_median) return(c(vector_output))}

source(“myfunc+ons.R”)àContentofmyfunc+ons.Rloadedintheuserworkspace(globalenvironment)

myfunc+ons.R

RStudio

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WhatisRstudio?•  FreeandopensourceIDE(IntegratedDevelopmentEnvironment)forR

•  AvailableforWindows,MacOSandLinux•  Wri]eninC++•  Firstbetaversionavailablein2009

•  Userfriendlyenvironment

RStudio

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Screen:4windowsRStudio

3.Environmentandhistory

1.Console 4.Files,plots,packages,help

2.Rscript

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RStudio

1.Console

Console:Interac+veenvironment.àWheretheworkisdone.Averyintui+veterminal!

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RStudio

2.Rscript

Savedscript

Canberunen+rely

Canberunbyline/block

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RStudio

3.Environmentandhistory

Globalenvironment:allobjectspresentinthesession

Youcanalso:SavethecurrentworkspaceLoadasavedworkspaceImportdatasets

Listfunc+onsavailableperpackage

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RStudio

3.Environmentandhistory

History:Commandsusedduringthesession.Canberunagain,copiedintofile,etc.

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RStudio

4.Plotarea

DisplaysthegraphsYoucan:•  Gobacktothepreviousplot•  Zoom•  Exportintopdf,jpeg,png,+ff,etc.

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RStudio

4.Files

Directoriesandfilesincurrentworkingdirectory

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RStudio

4.Packages

Listofpackages:•  Available•  Loadedincurrentsession(+cked)

Youcan:•  Installnewpackages•  Updatepackagestonewestversions

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RStudio

4.Help

Helptab:•  RandRStudiodocumenta+on•  Packagesandfunc+onshelppage

displayedherewhenrequested

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RMD:RMarkdown

•  Formatforwri)ngreproducible,dynamicreportswithR.

•  Workdirectlyinsertedintoforma]eddocuments(HTML,PDFandWord)

•  Easytouse!

RStudio

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RStudio

RMD:RMarkdown

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RStudio

RMD:RMarkdown

.Rmdextensionfiles

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RStudio

RMD:RMarkdown

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RStudio

RMD:RMarkdown

```{r}YOURCODE```

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RStudio

RMD:RMarkdown

echo=TRUEeval=TRUEcode+outputinreportecho=FALSEeval=TRUEonlyoutputinreport

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RStudio

RMD:RMarkdown

knitrpackagedynamicreportgenera)oninR

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RStudio

RMD:RMarkdown

KnittoHTMLàCreatesa.htmlfile

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Usefulresources

•  QuickR:h]p://www.statmethods.net/•  Rbloggers:h]p://www.r-bloggers.com/•  CookbookforR:h]p://www.cookbook-r.com/•  Rforgeforum:h]ps://r-forge.r-project.org/forum/forum.php?forum_id=78

•  Rhelp:h]p://r.789695.n4.nabble.com/R-help-f789696.html

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