Day 1 Challenges

RAdelaide 2024

Author
Affiliation

Dr Stevie Pederson

Black Ochre Data Labs
Telethon Kids Institute

Published

July 9, 2024

Some Challenges

Working With Text Strings

  1. Given a vector of Transcript IDs with versions, remove the version number?
ids <- c("ENST00000376207.10", "ENST00000376199.7")
  1. Add the ‘chr’ prefix to these chromosomes
chr <- c(1:22, "X", "Y", "M")
  1. Pull the chromosome out of these cytogenetic bands
cyto <- c("Xp11.23", "11q2.3", "2p7.1")
  1. Convert the following genes from human to mouse
genes <- c("FOXP3", "IL2RA", "CTLA4")
  1. Remove the suffix “.bam” from these filenames
bams <- c("rna_bamboo1.bam", "rna_rice1.bam", "rna_wheat1.bam")
  1. Correct the responses to be consistent (choose the format)
response <- c("Y", "yes", "No", "no")
  1. Load the pcr data using the following code then create create two additional columns
    1. treatment: containing the CONTROL/INFECTED status
    2. timepoint: with all times ending in ‘hr’
pcr <- read_excel("data/RealTimeData.xlsx") %>% 
  dplyr::rename(sample = `...1`)