#Section A — Arithmetic with Gene Expression Counts ## Q1. Add Two Gene Counts
Gene_A<-120
Gene_B<-200
Gene_A+Gene_B## [1] 320#Q2. Multiply Read Depths from Two Runs
Seq_1<-500000
Seq_2<-600000
Seq_1*Seq_2## [1] 3e+11#Q3. Calculate Fold-Change in Expression
Gene_X_control<-300
Gene_X_treated<-150
Gene_X_foldchange<-c(Gene_X_control/Gene_X_treated)
Gene_X_foldchange## [1] 2#Q4. Remainder of Reads per Lane
Sample_reads<-1001000
reads_per_lane<-250000
Remainder_per_lane<-Sample_reads%%reads_per_lane
Remainder_per_lane## [1] 1000#Q5. Store a Gene Count in a Variable
gene_x_count<-350
gene_x_count## [1] 350#Q6. Add Counts from Two Patients
Patient_A<-100
Patient_b<-120
Total_count<-Patient_A+Patient_b
Total_count## [1] 220#Q7. Update a Mistaken Value
Patient_A<-100
Patient_B_updated<-130
Updated_Total_count<-Patient_A+Patient_B_updated
Updated_Total_count## [1] 230#Q8. Store the Name of a Marker Gene
marker_gene<-"CD274"
marker_gene## [1] "CD274"##Q9. Check the Data Type of a Count
x<-100
class(x)## [1] "numeric"#Q10. Check the Type of a Gene Name
New_data<-"TP53"
class(New_data)## [1] "character"#Q11. Logical Flag for Marker Gene
is_marker<-TRUE
class(is_marker)## [1] "logical"#Q12. Create a Vector of Gene Counts
counts<-c(120,150,130)
counts## [1] 120 150 130#Q13. Assign Gene Names to Counts
names(counts)<-c("TP53", "BRCA1", "EGFR")#Q14.Print the Named Vector
counts## TP53 BRCA1 EGFR
## 120 150 130#Q15. Extract One Gene’s Count
counts["EGFR"]## EGFR
## 130#Q16. Extract the First Two Genes
counts[1:2]## TP53 BRCA1
## 120 150#Q17. Create Sample Names
vector<-c("Sample1","Sample2","Sample3")
vector## [1] "Sample1" "Sample2" "Sample3"#Q18. Combine Gene Names with Counts
genes <- c("TP53", "BRCA1", "EGFR")
counts <- c(120, 150, 130)
names(counts)<-genes
counts## TP53 BRCA1 EGFR
## 120 150 130#Q19. Check the Class of the Count Vector
class(counts)## [1] "numeric"#Q20. Create Patient IDs with Sequence
patient_IDs<-paste("patient",1:5,sep="_")
patient_IDs## [1] "patient_1" "patient_2" "patient_3" "patient_4" "patient_5"#Q21. What Happens in a Mixed Vector?
Vector_new<-c("TP53", 100, TRUE)
class(Vector_new)## [1] "character"#Q22. Convert a Character to Numeric
as.numeric("150")## [1] 150#Q23. Addition with Mixed Types (Fails)
x <- 5
y <- "6"
#x + y#Q24. Fix the Error and Add
Y<-as.numeric(y)
x+Y## [1] 11#Q25. Filter Genes with High Expression
counts <- c("TP53" = 120, "BRCA1" = 90, "EGFR" = 310)
counts[counts>100]## TP53 EGFR
## 120 310