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Noah L. Schrick 2022-08-30 15:46:24 -05:00
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Schrick-Noah_CS-6643_Lab1.R
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# Lab 1 for the University of Tulsa's CS-6643 Bioinformatics Course
# Introduction to R, Online bioinformatics resources, nucleotide frequency statistics
# Intro to R, online bioinformatics resources, nucleotide frequency statistics
# Professor: Dr. McKinney, Fall 2022
# Noah L. Schrick - 1492657
#### Part A: Seq Function
## a
AAvec <- seq(from = 1, to = 33, by = 2)
## b
ABvec <- seq(from = 7, to = 40, length.out = 15)
## c
my.dna <- sample(c("A", "C", "G", "T"), size = 20, replace = T)
## d
my.dna.A <- length(which(my.dna == "A"))
## e
my.dna.table <- table(my.dna)
my.dna.table.df <- as.data.frame(my.dna.table)
cols <- rainbow(nrow(my.dna.table))
my.dna.table.df$percent <-
round(100*my.dna.table.df$Freq/sum(my.dna.table.df$Freq), digits = 1)
my.dna.table.df$label <- paste(my.dna.table.df$my.dna,
" (", my.dna.table.df$percent, "%)", sep = "")
pie(my.dna.table.df$Freq, labels = my.dna.table.df$label, col = cols,
main = "Pie Chart Representation of Random ACTG Sample")
bp <- barplot(as.matrix(my.dna.table), beside = TRUE, xlab = "Letter",
ylab = "Frequency", ylim = c(-1, max(as.numeric(my.dna.table))+2),
main = "Bar Plot Representation of Random ACTG Sample", col = cols,
legend = TRUE)
text(x = bp, y = my.dna.table + 0.5, labels = as.numeric(my.dna.table))
text(x = bp, y = -0.5, labels = names(my.dna.table))
## f
my.dna2 <- sample(c("A", "C", "G", "T"), size = 20, replace = T,
prob = c(0.1, 0.4, 0.4, 0.1))
my.dna2.table <- table(my.dna2)
my.dna2.table
#### Part B: NCBI (no supporting R code for this part)