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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# `abnomic`: antibody profile immunomics project
<!-- badges: start -->
<!-- badges: end -->
The goal of `abnomic` is to provide a reproducible workflow for the undergraduate thesis project: "Comparación de la respuesta de anticuerpos ante _Plasmodium vivax_ en pacientes de la Amazonía Peruana según su severidad y episodios previos mediante microarreglos de proteínas".
## Outputs
- take a look at the approved [project](https://github.com/avallecam/abnomic/blob/main/01-project.pdf)
## To-Do
- ( ) create a `renv` environment
<!-- - ( ) [MUST] Reproducibility array - request to ADi -->
<!-- - ( ) [MUST] Peptides list - request to ADi -->
## Reproducibility
Dataset required:
+ for `03-sevrcov.Rmd`
- `data-raw/malaria severa 28Nov2014_Ed.dta`
- `data-raw/severe_malaria_vivax SEP2016.dta`
- `data-raw/samples.csv`
+ for `04-abnomic.Rmd`
- `data-raw/ADi-NAMRU6_Data-samples.csv`
- `data-raw/samples.csv`
- `data-raw/PfPv500_NonpresentReactiveTargets.xlsx`
+ for `04-abnomic.Rmd` generated after PlasmoDB strategy
- `data/04-listgen.tsv`
- `data/04-listall.tsv`
- `data/04-listgit.tsv`
- `data/00-protn6c.xlsx`
- `data/00-protn6c.xlsx`
### plasmodb search strategy
__whole genome__
- link: https://plasmodb.org/plasmo/app/workspace/strategies/import/1247ea53c4a464a3
- local route: data/20211013-02_whole_31ago2017-pvx_genome.txt
- characteristics:
+ 5665 genes
- variables:
+ Gene ID
+ Transcript ID
+ Product description
+ Gene name or symbol
__all genes by ID in microarray chip__
- link: https://plasmodb.org/plasmo/app/workspace/strategies/import/b32a1aefa2a27bbd
- local route: data/20211013-01_allgen_20ago2017-microarray_chip.txt
- characteristics:
+ 873 genes
+ 880 transcripts
- variables:
+ Same as previous, plus
+ Ortholog count
+ Gene variability (Total SNPs, NonSyn/Syn SNP ratio)
+ Protein extracellular localization and secretory pathways (# TM domains, SignalP scores)
+ Gene ontology (components, functions, processes)
+ Gene characteristics (# exons and transcripts, length of transcript, CDS and protein)
<!-- ## Related projects -->
<!-- - paper: epidemiological analysis of original case-control study -->
<!-- - paper: severe pv malaria ab response, only pv | combined pv + pf analysis -->
<!-- - ~~paper: previous exposure ab response (self-report with lot of biases)~~ -->
<!-- - paper: drug treatment related ab response -->