Data Science in Omics Introduction
An OMICS Course Part 1: Shell, Organizing and Genomics
A colleague has produced a file with one DNA sequence on each line. Download
the file. Load it into R withread.csv() and name the data frame sequences.
Your colleague wants to calculate the GC content of each DNA sequence (i.e., the
percentage of bases that are either G or C) and knows just a little R. They sent
you the following code, which will calculate the GC content for a single
sequence using the stringr package:
sequence <- "attggc"
num_g <- str_count(sequence, "g")
num_c <- str_count(sequence, "c")
gc_content <- (num_g + num_c) / str_length(sequence) * 100
Convert the last three lines of this code into a function to calculate the GC
content of a DNA sequence. Name that function get_gc_content.
Use a for loop and your function to calculate the GC content of each sequence
and store the results in a new data frame using an index. The following code will help you create this data frame:
# create an empty data frame with one row for each sequence
gc_contents <- data.frame(gc_content = numeric(nrow(_______)))
# loop over sequences using an index for the row and
# store the output in the new data frame
for (i in 1:nrow(__________)){
________[i,] <- get_gc_content(sequences$____[____])
}