https://github.com/sam-k/malaria-spat21-analysis
Cleaning and preliminary analysis of mosquito/blood data
https://github.com/sam-k/malaria-spat21-analysis
dataset genomics malaria
Last synced: about 2 months ago
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Cleaning and preliminary analysis of mosquito/blood data
- Host: GitHub
- URL: https://github.com/sam-k/malaria-spat21-analysis
- Owner: sam-k
- Created: 2018-12-29T03:24:45.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-08-25T04:48:18.000Z (over 5 years ago)
- Last Synced: 2025-01-27T13:16:04.712Z (4 months ago)
- Topics: dataset, genomics, malaria
- Language: R
- Homepage:
- Size: 25.3 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# malaria-spat21-analysis
Cleaning and preliminary analysis of descriptive and qPCR data from human blood and mosquitoes.
Part of the [Spatial R21 project](https://sites.duke.edu/taylorlab/projects/#MolEpi), which investigates the molecular epidemiology of *P. falciparum* transmission in Western Kenya.
## Preliminary mosquito data management
### Processing data
- Standardize column names and sample IDs of all datasets.
- Reformat the descriptive *Anopheles* dataset such that each row corresponds to a single mosquito.
- Censor the qPCR dataset by Ct values of human β-tubulin (Hbtub) and *Plasmodium* (Pfr364) targets, as well as by parasitemia.
### Cleaning data
- Correct formatting errors in household and sample IDs.
- Correct inconsistencies in village, household, and sample IDs within each sample.
- Correct inconsistencies in descriptions of each mosquito.
- Resolve duplicate entries of the same sample.
- Remove redundant columns.
### Merging data
- Sort all datasets.
- Create a dataset pairing mosquito descriptions with corresponding qPCR results.
- Identify missing entries between datasets.
- Tabulate mosquito counts per village, abdominal status, and species.
## Preliminary mosquito data analysis
## Preliminary human data management
## Collaborators
- [Kelsey Sumner](https://github.com/kelseysumner)