Remind students to install Bioconductor.

Remember to download Archaea genome data.

Set up R console:

source("https://bioconductor.org/biocLite.R")
biocLite("ShortRead")
library(ShortRead)

Lists

sites <- c("a", "b", "c")
notes <- "It was a good day in the field today. Warm, sunny, lots of gators."
helpers <- 4
field_notes <- list(sites, notes, helpers)
field_notes[1]
field_notes[[1]]
field_notes <- list(sites=sites, notes=notes, helpers=helpers)
field_notes$sites
field_notes[["sites"]]

Objects

Bioconductor

reads <- readFasta("data/archaea_dna/T-pendens.fasta")
reads
str(reads)

reads@sread
reads@sread[[1]]

reads@sread@ranges
reads@sread@ranges@start

sread(reads)
reverse(reads@sread)
complement(reads@sread)
reverseComplement(reads@sread)
alphabetFrequency(reads@sread)
translate(reads@sread)

Assign Exercise 6 - Multiple Files.