R formation
Session 1
Introduction to R and RStudio
- R introduction
- RStudio interface
- numerical operation
- data structure
- functions
- R packages
- Examples
Session 2
Introduction to tidyverse In this session we play-back the steps of the creation of an Exel table
- numerical variable creation
- numerical operations
- string creation
- variable concatenation and variable type: paste0, typeof
- vector : lenght, head, summary
- data.frame : dim, ncol, nrow
- matrix
- list
session 2
In this session we extract the list of differentially expressed genes from a DESeq2 .csv output. We then extract only the up-regulated and down-regulated genes.
- load a table: read.table, read.csv
- columns selection : boolean vector
- lines selection : boolean vector
- write a .csv and .Rdata file
- path, working-directory, and .Rhistory file
session 3
In this session we counts the nucleotides in a sequences
- load .Rdata object with the sequence
- transformation between vector and string : split
- loop
- simple conditional testing : if else
- code wrapping within function
- script
session n
Conversion of a fasta file into a GTF file
- list as hashing table
- regexp
session n+1
Converting a nucleotide sequence into a protein sequence
- load codon to AA table
- build conversion function between codon and AA
- build conversion function for a sequence function
- use list as hashing table