params <- list(isSlides = "no") ## ----include=FALSE------------------------------------------------------------ suppressPackageStartupMessages(require(knitr)) knitr::opts_chunk$set(echo = TRUE, tidy = T) ## ----xaringan-themer, include=FALSE, warning=FALSE---------------------------- library(xaringanthemer) style_mono_accent( base_color = "#23373B", header_font_google = google_font("Montserrat"), text_font_google = google_font("Fira Sans", "300", "300i"), code_font_google = google_font("Fira Code") ) ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides != "yes"){ cat("# Introduction to R (part 1) --- " ) } ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Set Up
--- " ) }else{ cat("# Set Up --- " ) } ## ----setwd_introtoR,eval=F---------------------------------------------------- ## setwd("/PathToMyDownload/Intro_To_R_1Day-master/r_course") ## # e.g. setwd("~/Downloads/Intro_To_R_1Day/r_course") ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Background of R
--- " ) }else{ cat("# Background of R --- " ) } ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Data Types in R
--- " ) }else{ cat("# Data Types in R --- " ) } ## ----simpleCalculations_introtoR,prompt=T------------------------------------- 3+1 2*2 sqrt(25)-1 ## ----usingFunctions_introtoR-------------------------------------------------- min(2,4,6) sum(2,4,6) max(2,4,6) ## ----usingFunctionsSQRT_introtoR---------------------------------------------- ?sqrt ## ----usingFunctionsArgOrder_introtoR------------------------------------------ min(5,4,6) min(6,4,5) ## ----usingFunctionsSetNames_introtoR,eval=F----------------------------------- ## dir() ## dir(full.names=T) ## ----usingFunctionsDefaultOrder_introtoR,eval=F------------------------------- ## dir(full.names=T) ## # Is equivalent to... ## dir(".",NULL,FALSE,T) ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Variables
--- " ) }else{ cat("# Variables --- " ) } ## ----variablesDefine_introtoR------------------------------------------------- x <- 10 ## ----variableHold_introtoR---------------------------------------------------- x ## ----variableShowForAlterInPlace_introtoR------------------------------------- x ## ----variableAlterInPlace_introtoR-------------------------------------------- x <- 20 x ## ----variableAsValueTheyContain_introtoR-------------------------------------- x ## ----variableAsValueFromFunTheyContain_introtoR------------------------------- x + sqrt(25) ## ----variableCreateNewVariable_introtoR--------------------------------------- y <- x + sqrt(25) y ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Vectors
--- " ) }else{ cat("# Vectors --- " ) } ## ----vectorBasic_introtoR----------------------------------------------------- x length(x) ## ----vectorCreate_introtoR---------------------------------------------------- x <- c(1,2,3,4,5,6,7,8,9,10) x length(x) ## ----vectorSeqFromColon_introtoR---------------------------------------------- y <- 6:10 y ## ----vectorSeqFromSeqAndRep_introtoR------------------------------------------ seq(from=1,to=5,by=2) rep(c(1,5,10),3) ## ----vectorIndexing_introtoR-------------------------------------------------- z <- seq(from=2,to=20,by=2) z z[1] z[8] ## ----vectorIndexingBy2_introtoR----------------------------------------------- z[c(1,6)] ## ----vectorIndexingByNeg_introtoR--------------------------------------------- z[-5] ## ----vectorIndexingAndReplace_introtoR---------------------------------------- z z[5] <- 1000 z ## ----vectorIndexingUsingVectors_introtoR-------------------------------------- y z[y] <- 0 z ## ----RememberSquareForIndex_introtoR------------------------------------------ x[1] ## ----RememberRoundForFunctions_introtoR--------------------------------------- sqrt(4) ## ----vectorArithmetricOperations_introtoR------------------------------------- x <- c(1,2,3,4,5,6,7,8,9,10) x y <- x*2 y ## ----vectorArithmetricOperationsMultipleVectors_introtoR---------------------- x+y ## ----vectorRecycle_introtoR--------------------------------------------------- x <- c(1,2,3,4,5,6,7,8,9,10) x x+c(1,2) ## ----vectorShorterRecycle_introtoR-------------------------------------------- x+c(1,2,3) ## ----vectorCharacters_introtoR------------------------------------------------ y <- c("ICTEM","CommonWealth","Wolfson") y[2] ## ----vectorCharacterNames_introtoR-------------------------------------------- x <- c(1:3) names(x) <- y x ## ----vectorCharacterNamesIndex_introtoR--------------------------------------- x[c("ICTEM","Wolfson")] ## ----vectorCharacterNamesIndexMissing_introtoR-------------------------------- x[c("Strand")] ## ----vectorUnique_introtoR---------------------------------------------------- geneList <- c("Gene1","Gene2","Gene3","Gene4","Gene5","Gene1","Gene3") unique(geneList) ## ----vectorLogical_introtoR--------------------------------------------------- z <- c(TRUE,FALSE,TRUE,FALSE,TRUE,FALSE,TRUE,FALSE,TRUE,FALSE) # or z <- c(T,F,T,F,T,F,T,F,T,F) z ## ----vectorLogicalOtherVector_introtoR---------------------------------------- x <- 1:10 x[z] ## ----vectorInFuncion_introtoR------------------------------------------------- geneList <- c("Gene1","Gene2","Gene3","Gene4","Gene5","Gene1","Gene3") secondGeneList <- c("Gene5","Gene3") logical_index <- geneList %in% secondGeneList logical_index geneList[logical_index] ## ----vectorLogicalFromOperators_introtoR-------------------------------------- x <- 1:10 x > 5 x[x > 5] ## ----vectorLogicalCombine_introtoR-------------------------------------------- x <- 1:10 !x > 4 x > 4 & x < 7 x > 4 | x < 7 ## ----vectorLogicalCombineIndex_introtoR--------------------------------------- x <- 1:10 x x[x > 4 & x < 7] x[x > 4 & !x < 7] ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Matrices
--- " ) }else{ cat("# Matrices --- " ) } ## ----matricesCreate_introtoR-------------------------------------------------- narrowMatrix <- matrix(1:10, nrow=5, ncol=2) narrowMatrix wideMatrix <- matrix(1:10, nrow=2, ncol=5) wideMatrix ## ----matricesCreateByRow_introtoR--------------------------------------------- wideMatrix <- matrix(1:10, nrow=2, ncol=5) wideMatrix wideMatrixByRow <- matrix(1:10, nrow=2, ncol=5, byrow=TRUE) wideMatrixByRow ## ----matricesDim_introtoR----------------------------------------------------- dim(narrowMatrix) nrow(narrowMatrix) ncol(narrowMatrix) ## ----matricesCbind_introtoR--------------------------------------------------- x <- 1:5 y <- 11:15 z <- 21:22 newMatrix <- cbind(x,y) newMatrix ## ----matricesRbind_introtoR--------------------------------------------------- newerMatrix <- rbind(newMatrix,z) newerMatrix ## ----matricesJoinIncompatable_introtoR---------------------------------------- recycledMatrix2 <- matrix(1:5,ncol=2,nrow=3) recycledMatrix2 ## ----matricesJoinIncompatableClip_introtoR------------------------------------ recycledMatrix3 <- rbind(recycledMatrix2,c(1:5)) recycledMatrix3 ## ----matricesNames_introtoR--------------------------------------------------- namedMatrix <- matrix(1:10,ncol=5,nrow=2) colnames(namedMatrix) <- paste("Column",1:5,sep="_") rownames(namedMatrix) <- paste("Row",1:2,sep="_") namedMatrix ## ----matricesNamesColRow_introtoR--------------------------------------------- colnames(namedMatrix) rownames(namedMatrix) ## ----matricesIndexingShow_introtoR-------------------------------------------- narrowMatrix ## ----matricesIndexingExample_introtoR----------------------------------------- narrowMatrix[2,1] ## ----matricesIndexingExampleByCol_introtoR------------------------------------ narrowMatrix[,2] ## ----matricesIndexingExampleByRow_introtoR------------------------------------ narrowMatrix[3,] ## ----matricesIndexingExampleByMultipleRow_introtoR---------------------------- narrowMatrix[c(2,3),] ## ----matricesIndexingExampleByName_introtoR----------------------------------- colnames(narrowMatrix) <- paste("Column",1:2,sep="_") rownames(narrowMatrix) <- paste("Row",1:5,sep="_") narrowMatrix[,"Column_1"] narrowMatrix["Row_1",] narrowMatrix["Row_1","Column_1"] ## ----matricesIndexingExampleByLogic_introtoR---------------------------------- narrowMatrix narrowMatrix[,1] narrowMatrix[,1] < 5 ## ----matricesIndexingExampleByLogicRow_introtoR------------------------------- narrowMatrix[narrowMatrix[,1] < 5,] ## ----matricesArithmetric_introtoR--------------------------------------------- narrowMatrix narrowMatrix[1,1]+2 narrowMatrix[1,]+2 ## ----------------------------------------------------------------------------- mean(narrowMatrix) ## ----matricesReplace_introtoR------------------------------------------------- narrowMatrix narrowMatrix[1,1] <- 10 narrowMatrix[,2] <- 1 narrowMatrix ## ----matricesOneTypeOnlyNoError_introtoR,error=T------------------------------ narrowMatrix[,2] *2 ## ----matricesOneTypeOnlyExampleForError_introtoR------------------------------ narrowMatrix[1,1] <- "Not_A_Number" narrowMatrix ## ----matricesOneTypeOnlyWithError_introtoR,error=T---------------------------- narrowMatrix[,2] *2 ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Factors
--- " ) }else{ cat("# Factors --- " ) } ## ----factorsIntro_introtoR---------------------------------------------------- vectorExample <- c("male","female","female","female") factorExample <- factor(vectorExample) factorExample levels(factorExample) ## ----factorsSummaryFunction_introtoR------------------------------------------ summary(vectorExample) summary(factorExample) ## ----factorsDisplayOrder_introtoR--------------------------------------------- factorExample <- factor(vectorExample, levels=c("male","female")) factorExample summary(factorExample) ## ----factorsNominal_introtoR-------------------------------------------------- factorExample <- factor(vectorExample, levels=c("male","female")) factorExample[1] < factorExample[2] ## ----factorsOrdinal_introtoR-------------------------------------------------- factorExample <- factor(c("small","big","big","small"), ordered=TRUE,levels=c("small","big")) factorExample factorExample[1] < factorExample[2] ## ----factorsOrder_introtoR---------------------------------------------------- factorExample <- factor(c("small","big","big","small")) factorExample[1] <- c("big") factorExample factorExample[1] <- c("huge") factorExample ## ----factorsAddNew_introtoR--------------------------------------------------- levels(factorExample) <- c("big","small","huge") factorExample[1] <- c("huge") factorExample ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Data Frames
--- " ) }else{ cat("# Data Frames --- " ) } ## ----dataframesIntro_introtoR------------------------------------------------- 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 ## ----dataframesReplacement_introtoR------------------------------------------- dfExample dfExample[dfExample[,"Survival_Time"] > 10,] ## ----dataframesReplacementbyDollar_introtoR----------------------------------- dfExample <- data.frame(Name=patientName,Type=patientType,Survival_Time=survivalTime) dfExample$Survival_Time dfExample[dfExample$Survival_Time < 10,] ## ----dataframesIndexbyDollar_introtoR----------------------------------------- dfExample$Surv ## ----dataframesIndexbyName_introtoR, eval=F----------------------------------- ## dfExample[,"Surv"] ## ----dataframesNewbyDollar_introtoR------------------------------------------- dfExample dfExample$newColumn <- rep("newData",nrow(dfExample)) dfExample ## ----dataframesNoReplace_introtoR--------------------------------------------- dfExample[dfExample[,"Survival_Time"] < 10,"Survival_Time"] <- 0 dfExample ## ----dataframesNoReplaceString_introtoR--------------------------------------- dfExample[1,"Type"] <- "other" dfExample ## ----dataframesAndFactors_introtoR-------------------------------------------- dfExample <- data.frame(Name=patientName,Type=patientType, Survival_Time=survivalTime) levels(dfExample[,"Type"]) <- c(levels(dfExample[,"Type"]) , "other") dfExample[1,"Type"] <- "other" dfExample ## ----dataframesAndNoFactors_introtoR------------------------------------------ dfExample <- data.frame(Name=patientName, Type=patientType, Survival_Time=survivalTime, stringsAsFactors = T) dfExample[dfExample[,"Survival_Time"] < 10,"Name"] <- "patientX" dfExample ## ----dataframesAndNoFactors_introtoR2----------------------------------------- dfExample <- data.frame(Name=patientName, Type=patientType, Survival_Time=survivalTime, stringsAsFactors = F) dfExample[dfExample[,"Survival_Time"] < 10,"Name"] <- "patientX" dfExample ## ----dataframesOrder_introtoR------------------------------------------------- testOrder <- c(20,10,30) testOrder order(testOrder,decreasing=T) ## ----------------------------------------------------------------------------- testOrder[order(testOrder)] testOrder[order(testOrder,decreasing=T)] ## ----dataframesOrderWithNA_introtoR------------------------------------------- testOrder <- c(2,1,NA,3) testOrder[order(testOrder,decreasing=T,na.last=T)] testOrder[order(testOrder,decreasing=T,na.last=F)] ## ----dataframesOrderDecreasing_introtoR--------------------------------------- dfExample dfExample[order(dfExample$Surv, decreasing=T),] ## ----dataframesOrderMultiple_introtoR----------------------------------------- dfExample[order(dfExample$Type, dfExample$Survival, decreasing=T),] ## ----dataframesMergeData1_introtoR-------------------------------------------- dfExample <- data.frame(Name=patientName,Type=patientType, Survival_Time=survivalTime) dfExample ## ----dataframesMergeData2_introtoR-------------------------------------------- dfExample2 <- data.frame(Name=patientName[1:3], height=c(6.1,5.1,5.5)) dfExample2 ## ----dataframesMerge_introtoR------------------------------------------------- mergedDF <- merge(dfExample,dfExample2,by=1,all=F) mergedDF ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Lists
--- " ) }else{ cat("# Lists --- " ) } ## ----listsExample_introtoR---------------------------------------------------- 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")) ## ----listsCreate_introtoR----------------------------------------------------- myList <- list(firstElement,secondElement,thirdElement) myList ## ----listsCreateNnames_introtoR----------------------------------------------- myNamedList <- list(First=firstElement,Second=secondElement, Third=thirdElement) myNamedList ## ----listsCreateElements_introtoR--------------------------------------------- myList <- list(firstElement,secondElement,thirdElement) myList[1] myList[[1]] ## ----listsIndexElements_introtoR---------------------------------------------- myNamedList$First ## ----listsCombine_introtoR---------------------------------------------------- myNamedList <- list(First=firstElement,Second=secondElement, Third=thirdElement) myNamedList <- c(myNamedList,list(fourth=c(4,4))) myNamedList[c(1,4)] ## ----listsCombineVector_introtoR---------------------------------------------- myList <- c(myList,c(4,4)) myList[3:5] ## ----listsFlatten_introtoR---------------------------------------------------- myNamedList <- list(First=c(1,2,3),Second=c(2,6,7),Third=c(1,4,7)) myNamedList flatList <- unlist(myNamedList) flatList[1:7] ## ----listsFlattenToMatrix_introtoR-------------------------------------------- myNamedList <- list(First=c(1,2,3),Second=c(2,6,7),Third=c(1,4,7)) flatList <- unlist(myNamedList) listAsMat <- matrix(flatList, nrow=length(myNamedList), ncol=3, byrow=T, dimnames=list(names(myNamedList))) listAsMat ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Coercing data classes
--- " ) }else{ cat("# Coercing data formats --- " ) } ## ----------------------------------------------------------------------------- class(namedMatrix) class(dfExample) ## ----------------------------------------------------------------------------- namedMatrix as.character(namedMatrix) as.vector(namedMatrix) ## ----------------------------------------------------------------------------- as.data.frame(namedMatrix) as.list(namedMatrix) ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat("class: inverse, center, middle # Reading and Writing Data
--- " ) }else{ cat("# Reading and Writing Data --- " ) } ## ----echo=F------------------------------------------------------------------- minRep <- rbind(cbind(matrix(rnorm(12,4),ncol=3,byrow = T),matrix(c(rnorm(9,4),rnorm(3,8)),ncol=3,byrow = T)), cbind(matrix(rnorm(12,10),ncol=3,byrow = T),matrix(c(rnorm(6,3),rnorm(6,10)),ncol=3,byrow = T))) colnames(minRep) <- paste0(c("Sample_"), 1:5,".",sort(rep(c("hi","low"),3))) minRepdf <- data.frame(Gene_Name=paste("Gene",letters[1:8],sep="_"),minRep) #minRepdf$Gene_Name <- paste("Gene",letters[1:8],sep="_") #write.table(minRepdf,file="readThisTable.csv",sep=",",row.names=F) kable(minRepdf[,1:4], format='html') ## ----echo=T------------------------------------------------------------------- Table <- read.table("data/readThisTable.csv",sep=",",header=T) Table[1:4,1:3] ## ----echo=T------------------------------------------------------------------- Table <- read.table("data/readThisTable.csv",sep=",",header=T,row.names=1) Table[1:4,1:3] ## ----echo=T------------------------------------------------------------------- Table <- read.table("data/readThisTable.csv", sep=",", header=T, stringsAsFactors=F) ## ----echo=T------------------------------------------------------------------- URL <- "http://rockefelleruniversity.github.io/readThisTable.csv" Table <- read.table(URL,sep=",",header=T) Table[1:2,1:3] ## ----eval=F------------------------------------------------------------------- ## Table <- read.table(file="clipboard",sep=",",header=T) ## ----echo=T------------------------------------------------------------------- x <- scan("data/readThisTable.csv",sep=",", what = c("character",rep("numeric", 6)),skip=1) x[1:3] ## ----echo=T------------------------------------------------------------------- write.table(Table, file="data/writeThisTable.csv", sep=",") ## ----echo=T------------------------------------------------------------------- write.table(Table, file="data/writeThisTable.csv", sep=",", row.names =F, col.names=T) ## ----------------------------------------------------------------------------- head(Table) ## ----------------------------------------------------------------------------- tail(Table) head(Table,3) ## ----echo=T,eval=FALSE-------------------------------------------------------- ## install.packages("rio") ## ----echo=T,eval=TRUE--------------------------------------------------------- library("rio") ## ----echo=T,eval=TRUE--------------------------------------------------------- Table <- import("data/readThisTable.csv") Table[1:2,] ## ----echo=T,eval=TRUE--------------------------------------------------------- Table <- import("data/readThisXLS.xls", which=2) Table <- import("data/readThisXLS.xls", which="Metadata") Table[1:2,] ## ----echo=T,eval=TRUE--------------------------------------------------------- Table <- import_list("data/readThisXLS.xls") names(Table) ## ----echo=T,eval=TRUE--------------------------------------------------------- ## Table[["ExpressionScores"]][1:2,] Table$ExpressionScores[1:2,] Table$Metadata[1:2,] ## ----echo=T,eval=TRUE--------------------------------------------------------- ExpressionScores <- Table$ExpressionScores export(ExpressionScores,file = "data/writeThisXLSX.xlsx") ## ----echo=T,eval=TRUE--------------------------------------------------------- names(Table) <- c("expr","meta") export(Table,file = "data/writeThisMultipleXLSX.xlsx")