diff --git a/session_4/session_4.Rmd b/session_4/session_4.Rmd index 88e4e55ab8da0c6e8c1bb67d76debccec36f6775..204770fed9d55e287f2206fd75cb035bc9672508 100644 --- a/session_4/session_4.Rmd +++ b/session_4/session_4.Rmd @@ -1,16 +1,22 @@ --- title: "R.4: data transformation" author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr), Hélène Polvèche [hpolveche@istem.fr](mailto:hpolveche@istem.fr)" -date: "2021" +date: "2022" output: rmdformats::downcute: self_contain: true use_bookdown: true default_style: "light" lightbox: true - css: "http://perso.ens-lyon.fr/laurent.modolo/R/src/style.css" + css: "../www/style_Rmd.css" --- +```{r include=FALSE} +library(fontawesome) +``` + + `r fa(name = "fas fa-house", fill = "grey", height = "1em")`  https://can.gitbiopages.ens-lyon.fr/R_basis/ + ```{r setup, include=FALSE} rm(list=ls()) knitr::opts_chunk$set(echo = TRUE) @@ -429,7 +435,7 @@ mutate( - Logical comparisons, `<`, `<=`, `>`, `>=`, `!=`, and `==` - Ranking: there are a number of ranking functions, but you should start with `min_rank()`. There is also `row_number()`, `dense_rank()`, `percent_rank()`, `cume_dist()`, `ntile()` -## See you in [R#5: Pipping and grouping](http://perso.ens-lyon.fr/laurent.modolo/R/session_5/) +## See you in [R#5: Pipping and grouping](https://can.gitbiopages.ens-lyon.fr/R_basis/session_5/) @@ -494,13 +500,13 @@ For the next part, we will use a real data set. Anterior tibial muscle tissue wa First, we will use the gene count table of these samples, formatted for use in ggplot2 ( `pivot_longer()` [function](https://tidyr.tidyverse.org/reference/pivot_longer.html) ). -Open the csv file using the `read_csv2()` function. The file is located at "http://perso.ens-lyon.fr/laurent.modolo/R/session_4/Expression_matrice_pivot_longer_DEGs_GSE86356.csv". +Open the csv file using the `read_csv2()` function. The file is located at "https://can.gitbiopages.ens-lyon.fr/R_basis/session_4/Expression_matrice_pivot_longer_DEGs_GSE86356.csv". <details><summary>Solution</summary> <p> ```{r read_csv1} -expr_DM1 <- read_csv2("http://perso.ens-lyon.fr/laurent.modolo/R/session_4/Expression_matrice_pivot_longer_DEGs_GSE86356.csv") +expr_DM1 <- read_csv2("https://can.gitbiopages.ens-lyon.fr/R_basis/Expression_matrice_pivot_longer_DEGs_GSE86356.csv") expr_DM1 ``` @@ -577,13 +583,13 @@ ggplot(expr_DM1, aes(samples, Genes, fill= log1p(counts))) + For this last exercise, we will use the results of the differential gene expression analysis between DM1 vs WT conditions. -Open the csv file using the `read_csv2()` function. The file is located at "http://perso.ens-lyon.fr/laurent.modolo/R/session_4/EWang_Tibialis_DEGs_GRCH37-87_GSE86356.csv". +Open the csv file using the `read_csv2()` function. The file is located at "http://can.gitbiopages.ens-lyon.fr/R_basis/session_4/EWang_Tibialis_DEGs_GRCH37-87_GSE86356.csv". <details><summary>Solution</summary> <p> ```{r read_csv2} -tab <- read_csv2("http://perso.ens-lyon.fr/laurent.modolo/R/session_4/EWang_Tibialis_DEGs_GRCH37-87_GSE86356.csv") +tab <- read_csv2("http://can.gitbiopages.ens-lyon.fr/R_basis/session_4/EWang_Tibialis_DEGs_GRCH37-87_GSE86356.csv") tab ```