Reading and writing data in R

 

These exercises are about the vector sections of Introduction to R.

Exercise 1

Have a look at all files in notepad or excel before attempting to read. All files can be found in the “data” directory.

• Read in the tab delimited file “GeneExpression.txt”.

geneExpression <- read.table("data/GeneExpression.txt",h=T,sep="\t",row.names=1)

• Find the mean expression of all samples.

sampleMeans <- c(mean(geneExpression[,1]),mean(geneExpression[,2]),mean(geneExpression[,3]),mean(geneExpression[,4]),mean(geneExpression[,5]),mean(geneExpression[,6]))
names(sampleMeans) <- colnames(geneExpression)
sampleMeans

##  Sample_1.hi  Sample_2.hi  Sample_3.hi Sample_4.low Sample_5.low Sample_1.low 
##     7.514996     6.774108     6.508127     6.262253     6.177761     6.017462

# Alternatively we could use the colMeans() function.
colMeans(geneExpression)

##  Sample_1.hi  Sample_2.hi  Sample_3.hi Sample_4.low Sample_5.low Sample_1.low 
##     7.514996     6.774108     6.508127     6.262253     6.177761     6.017462

• Read in the tab delimited file “GeneExpressionWithMethods.txt”. This file contains information on analysis steps used to produce file.

geneExpression <- read.table("data/GeneExpressionWithMethods.txt",h=T,sep="\t",row.names=1,skip=3)
geneExpression

##        Sample_1.hi Sample_2.hi Sample_3.hi Sample_4.low Sample_5.low
## Gene_a    5.742510    3.214303    4.116820     3.212353     5.742333
## Gene_b    6.444368    5.896076    2.592581     5.089549     3.624812
## Gene_c    3.083392    3.414723    3.706069     4.535536     5.104273
## Gene_d    4.726498    3.023746    3.033173     8.017895     8.098800
## Gene_e    9.909185    9.174323    9.957153     2.053501     3.276533
## Gene_f   10.680459    9.951243    8.985412     3.360963     3.566663
## Gene_g   10.516534   10.176163    9.778173    11.781520     9.005437
## Gene_h    9.017020    9.342291    9.895636    12.046704    11.003240
##        Sample_1.low
## Gene_a    5.9350948
## Gene_b    2.6313925
## Gene_c    5.7149521
## Gene_d    8.1964109
## Gene_e    0.7332521
## Gene_f    3.8519471
## Gene_g   11.1733928
## Gene_h    9.9032500

• Read in the tab delimited file “GeneExpressionWithNotes.txt”. This file contains notes about particular genes.

geneExpression <- read.table("data/GeneExpressionWithNotes.txt",h=T,sep="\t",row.names=1,comment.char = ">")
geneExpression

##        Sample_1.hi Sample_2.hi Sample_3.hi Sample_4.low Sample_5.low
## Gene_a    5.742510    3.214303    4.116820     3.212353     5.742333
## Gene_b    6.444368    5.896076    2.592581     5.089549     3.624812
## Gene_c    3.083392    3.414723    3.706069     4.535536     5.104273
## Gene_d    4.726498    3.023746    3.033173     8.017895     8.098800
## Gene_e    9.909185    9.174323    9.957153     2.053501     3.276533
## Gene_f   10.680459    9.951243    8.985412     3.360963     3.566663
## Gene_g   10.516534   10.176163    9.778173    11.781520     9.005437
## Gene_h    9.017020    9.342291    9.895636    12.046704    11.003240
##        Sample_1.low
## Gene_a    5.9350948
## Gene_b    2.6313925
## Gene_c    5.7149521
## Gene_d    8.1964109
## Gene_e    0.7332521
## Gene_f    3.8519471
## Gene_g   11.1733928
## Gene_h    9.9032500

• Read in tab delimited file “GeneExpression.txt”. Order genes by decreasing expression in Sample_1.hi. Write out a new comma separated file with column titles.

geneExpression <- read.table("data/GeneExpression.txt",h=T,sep="\t",row.names=1)
orderedExpression <- geneExpression[order(geneExpression$Sample_1.hi,decreasing=T),]
expressionDF <- cbind(rownames(orderedExpression),orderedExpression)
colnames(expressionDF)[1] <- "geneNames"
write.table(expressionDF,"orderedExpression.txt",sep=",",col.names = T,row.names=F)