Matrices answers

These exercises cover the matrices sections of Introduction to R.

Exercise 1

• Create a matrix containing information on gene names Gene_1, Gene_2, Gene_3,Gene_4 expression values 1000, 3000, 10000, 12000 and gene lengths 100, 3000, 200, 1000

geneNames <- c("Gene_1", "Gene_2", "Gene_3","Gene_4")
expression <- c(1000, 3000, 10000, 12000)
geneLengths <- c(100, 3000, 200, 1000)
geneMatrix <- cbind(expression,geneLengths)
rownames(geneMatrix) <- geneNames
geneMatrix

##        expression geneLengths
## Gene_1       1000         100
## Gene_2       3000        3000
## Gene_3      10000         200
## Gene_4      12000        1000

• Update the matrix to contain the expression over the gene length for all genes (Length normalised expression) as final column.

lne <- geneMatrix[,"expression"]/geneMatrix[,"geneLengths"]
geneMatrix <- cbind(geneMatrix,lne)
geneMatrix

##        expression geneLengths lne
## Gene_1       1000         100  10
## Gene_2       3000        3000   1
## Gene_3      10000         200  50
## Gene_4      12000        1000  12

• Create a smaller matrix containing genes longer than 200

smallGeneMatrix <- geneMatrix[geneMatrix[,"geneLengths"] > 200,]
smallGeneMatrix

##        expression geneLengths lne
## Gene_2       3000        3000   1
## Gene_4      12000        1000  12

• Create a smaller matrix with just expression and lne columns containing genes longer than 200 and expression greater than 3000.

smallGeneMatrix <- geneMatrix[geneMatrix[,"geneLengths"] > 200 & geneMatrix[,"expression"] > 200,c("expression","lne")]
smallGeneMatrix

##        expression lne
## Gene_2       3000   1
## Gene_4      12000  12

• Calculate the sum of expression and length columns for only genes with length > 100.

expressionSum <- sum(geneMatrix[geneMatrix[,"geneLengths"] > 100,"expression"])
geneLengthSum <- sum(geneMatrix[geneMatrix[,"geneLengths"] > 100,"geneLengths"])
#OR
expressionAndGeneLengthSum <- colSums(geneMatrix[geneMatrix[,"geneLengths"] > 100,c("expression","geneLengths")])
expressionAndGeneLengthSum

##  expression geneLengths 
##       25000        4200