Quiz - R Tutorial - Reading & analyzing data

To answer the quiz questions, download and read the Arabidopsis TAIR10 annotations for protein-coding genes, using the same methods you used for the Camelina data. (The file format is the same.)

This file contains annotations for protein-coding genes in Arabidopsis.

After running the following code, use the genes data frame to answer the questions.

Code:

root="http://igbquickload.org/quickload/A_thaliana_Jun_2009"
file_name="TAIR10_mRNA.bed.gz"
URL=paste(root,file_name,sep="/")
download.file(url=URL,destfile=file_name)
data = read.delim(file_name,as.is=T,sep="\t",header=FALSE,quote="")
genes = data[,c(1,2,3,4,6,10,13,14)]
column_names=c("chr","start","end","id","strand","num_exons",
               "locus","description")
names(genes)=column_names