Saideep Gona
March 16, 2023
suppressMessages(library(tidyverse))
suppressMessages(library(glue))
PRE = "C:\\Users\\Saideep\\Box\\imlab-data\\data-Github\\Daily-Blog-Sai"
## COPY THE DATE AND SLUG fields FROM THE HEADER
SLUG="updating-existing-geuvadis-analysis" ## copy the slug from the header
bDATE='2023-03-16' ## copy the date from the blog's header here
DATA = glue("{PRE}/{bDATE}-{SLUG}")
if(!file.exists(DATA)) system(glue::glue("mkdir {DATA}"))
WORK=DATAAfter debugging the merged pipeline I reran the GEUVADIS data and replicated the Kircher mutagenesis as a test of the quantification (which I also optimized a bit). I also quantified the GEUVADIS data, so the tables are now ready to be used to re-run the prior GEUVADIS analyses. I am also in the process of moving over these analyses to the lab github and box. Yesterday I did some preparation for upcoming TAship, but today I am moving on to updating the GEUVADIS analyses
The first analysis to update is the portability analysis.
---
title: "Updating Existing GEUVADIS Analyses"
author: "Saideep Gona"
date: "2023-03-16"
format:
html:
code-fold: true
code-summary: "Show the code"
execute:
freeze: true
warning: false
---
```{r}
#| label: Set up box storage directory
suppressMessages(library(tidyverse))
suppressMessages(library(glue))
PRE = "C:\\Users\\Saideep\\Box\\imlab-data\\data-Github\\Daily-Blog-Sai"
## COPY THE DATE AND SLUG fields FROM THE HEADER
SLUG="updating-existing-geuvadis-analysis" ## copy the slug from the header
bDATE='2023-03-16' ## copy the date from the blog's header here
DATA = glue("{PRE}/{bDATE}-{SLUG}")
if(!file.exists(DATA)) system(glue::glue("mkdir {DATA}"))
WORK=DATA
```
# Context
After debugging the merged pipeline I reran the GEUVADIS data and replicated the Kircher mutagenesis as a test of the quantification (which I also optimized a bit). I also quantified the GEUVADIS data, so the tables are now ready to be used to re-run the prior GEUVADIS analyses. I am also in the process of moving over these analyses to the lab github and box. Yesterday I did some preparation for upcoming TAship, but today I am moving on to updating the GEUVADIS analyses
## Portability Analysis
The first analysis to update is the portability analysis.