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LBMC
RMI2
TDD_project
Commits
f5fc2c69
Commit
f5fc2c69
authored
1 year ago
by
dcluet
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Add explanation for column name changes
parent
850aeba1
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README.md
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-12
43 additions, 12 deletions
README.md
RMI2_Random_Forest.Rmd
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-2
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RMI2_Random_Forest.Rmd
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README.md
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f5fc2c69
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@@ -100,20 +100,51 @@ The final arborescence should be:
...
@@ -100,20 +100,51 @@ The final arborescence should be:
*
filtred_genes_Lympho_Activated.csv
*
filtred_genes_Lympho_Activated.csv
*
DESeqresults_lympho_activation_untreated.csv
*
DESeqresults_lympho_activation_untreated.csv
> The `filtred_genes_Lympho_Resting.csv` and
> **NOTA BENE**
> `filtred_genes_Lympho_Activated.csv` files
> are used to focus the machine learning process on pre-selected transcripts.
>
>
> This selection was based on the gene normalized read counts of the 3h
> **The `filtred_genes_Lympho_Resting.csv` and**
> Triptolide libraries (~5000 genes in Resting and ~6000 genes in Activated
> **`filtred_genes_Lympho_Activated.csv` files**
> T-cells). Of these, only genes with completed observations in all biological
> **are used to focus the machine learning process on pre-selected transcripts.**
> replicates (including ribosome profiling libraries) and for all
> transcript features used to build the model, as well as at least 15% of
> observed degradation at 3h, were kept for further analysis.
>
>
> The `DESeqresults_lympho_activation_untreated.csv` file is used to add the
> **This selection was based on the gene normalized read counts of the 3h**
> `log2FoldChange` to the database.
> **Triptolide libraries (~5000 genes in Resting and ~6000 genes in Activated**
> This column is used as parameter for the `deltaTDD` and `deltaTID` scores.
> **T-cells). Of these, only genes with completed observations in all biological**
> **replicates (including ribosome profiling libraries) and for all**
> **transcript features used to build the model, as well as at least 15% of**
> **observed degradation at 3h, were kept for further analysis.**
>
> **The `DESeqresults_lympho_activation_untreated.csv` file is used to add the**
> **`log2FoldChange` to the database.**
> **This column is used as parameter for the `deltaTDD` and `deltaTID` scores.**
>
> **Has we had a lot of experimental conditions and time. Scores required**
> **to "explicitely" indicate how they have been obtained.**
> **In order to have the optimal tracking of which experimental data have been**
> **used as input and how (we had initially several metrics: relative,**
> **absolute, ...). Thus I generated some "complex" column names allowing to**
> **precisely use the correct column and can be handled without any**
> **modification by `Python` pandas library. For exemple the**
> **$TDD_{index}$ column name**
> **is [initialy](https://gitbio.ens-lyon.fr/LBMC/RMI2/rmi2_gff_fasta_compilation):**
>
> `Abs(TDD)>Lympho_Resting>Trip_CHX>Ref_Trip_0h>3h`
>
> **Meaning that the `Absolute TDD` score has been computed for (`>`)**
> **the `Lympho` in the `Resting` status using (`>`) the `Trip_CHX` treatment**
> **condition, with the `Trip` treatment condition at `0h` as reference `Ref`,**
> **and computed with `>` t = `3h`.**
>
> **Nevertheless due to restrictions in column names in `R`, some characters like**
> **`()` and `>`. Thus, Emmanuel Labaronne had to change such names to**
> **perform `Random Forest` computations with `R`.**
> **This column is now called:**
>
> `Abs.TDD..Lympho_Resting.Trip_CHX.Ref_Trip_0h.3h`
>
> **Once the reviewing process will be over, I will change the**
> **[initial](https://gitbio.ens-lyon.fr/LBMC/RMI2/rmi2_gff_fasta_compilation)**
> **`Python` scripts to take into account the downstream `R` limitations.**
## Generate a Random Forest model
## Generate a Random Forest model
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RMI2_Random_Forest.Rmd
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@@ -38,7 +38,7 @@ header-includes:
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@@ -38,7 +38,7 @@ header-includes:
\includegraphics[width=1cm]{Logos/logo-rmi2-lab-version-2.png}
\includegraphics[width=1cm]{Logos/logo-rmi2-lab-version-2.png}
}
}
- \cfoot{\thepage}
- \cfoot{\thepage}
- \lfoot{Written by Labaronne Emmanuel and Cluet David
,
current version 2023/12/06}
- \lfoot{Written by Labaronne Emmanuel and Cluet David
\newline
current version 2023/12/06}
- \renewcommand{\footrulewidth}{0.4pt}
- \renewcommand{\footrulewidth}{0.4pt}
- \pretitle{\begin{center}
- \pretitle{\begin{center}
\includegraphics[width=2cm,height=2cm]{Logos/logo-rmi2-lab-version-2.png}\LARGE\\}
\includegraphics[width=2cm,height=2cm]{Logos/logo-rmi2-lab-version-2.png}\LARGE\\}
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@@ -93,7 +93,7 @@ source("src/randomForest.R")
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@@ -93,7 +93,7 @@ source("src/randomForest.R")
## Fine grain tuning of the Random Forest model
## Fine grain tuning of the Random Forest model
```{r do_RF}
```{r do_RF
_please_wait
}
# Perform the random forest
# Perform the random forest
model <- makeRandomForest(x = x,
model <- makeRandomForest(x = x,
explicit_x = x_explicit)
explicit_x = x_explicit)
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