Factors and Data frames

 

These exercises are about the factors and data frames sections of Introduction to R.

Exercise 1 - Data frames

• Create data frame called Annotation with a column of gene names (“Gene_1”, “Gene_2”, “Gene_3”,“Gene_4”,“Gene_5”), ensembl gene names (“Ens001”, “Ens003”, “Ens006”, “Ens007”, “Ens010”), pathway information (“Glycolysis”, “TGFb”, “Glycolysis”, “TGFb”, “Glycolysis”) and gene lengths (100, 3000, 200, 1000,1200).

• Create data frame called Sample1 with ensembl gene names (“Ens001”, “Ens003”, “Ens006”, “Ens010”) and expression (1000, 3000, 10000,5000)

• Create data frame called Sample2 with ensembl gene names (“Ens001”, “Ens003”, “Ens006”, “Ens007”,“Ens010”) and expression (1500, 1500, 17000,500,10000)

• Create a data frame containing only those gene names common to all data frames with all information from Annotation and the expression from Sample 1 and Sample 2.

##   ensembl geneNames    pathway geneLengths expression.x expression.y
## 1  Ens001    Gene_1 Glycolysis         100         1000         1500
## 2  Ens003    Gene_2       TGFb        3000         3000         1500
## 3  Ens006    Gene_3 Glycolysis         200        10000        17000
## 4  Ens010    Gene_5 Glycolysis        1200         5000        10000

• Add an extra two columns containing the length normalised expressions for Sample 1 and Sample 2.

Hint see our previous exercises

##   ensembl geneNames    pathway geneLengths expression.x expression.y
## 1  Ens001    Gene_1 Glycolysis         100         1000         1500
## 2  Ens003    Gene_2       TGFb        3000         3000         1500
## 3  Ens006    Gene_3 Glycolysis         200        10000        17000
## 4  Ens010    Gene_5 Glycolysis        1200         5000        10000
##   Sample1_lne Sample2_lne
## 1   10.000000   15.000000
## 2    1.000000    0.500000
## 3   50.000000   85.000000
## 4    4.166667    8.333333

• Identify the mean length normalised expression across Sample1 and Sample2 for Ens006 genes

## [1] 50

• For all genes, identify the log2 fold change in length normalised expression from Sample 1 to Sample 2.

##     Gene_1     Gene_2     Gene_3     Gene_5 
##  0.5849625 -1.0000000  0.7655347  1.0000000

• Identify the total length of genes in Glycolysis pathway.

## [1] 1500