UW_Adult_Covid-19

This project repository contains R packages and scripts to generate results for the paper entitled "The landscape of antibody binding in SARS-CoV-2 infection"

Processing peptide arrays and MUSCLE alignments

Please see https://dholk.primate.wisc.edu/project/dho/sequencing/Polypeptide%20Microarrays/public/COVID_19/begin.view for data and instructions for preprocesing the peptide binding array data and MUSCLE (MUltiple Sequence Comparison by Log-Expectation) alignments for comparing each coronavirus to the Wu1-SARS2 sequence. To run the find_wu1_epitopes.Rmd script, you don't need to be able to run pepMeld, you can download the "aggregated_data/df_stacked.tsv.gz" and "all_sequences_except_wi.tsv.gz" from the above website and run the find_wu1_epitopes.Rmd mentioned below. See find_wu1_epitopes.Rmd for details.

ELISA Array Correlation (Figure 6)

Data for correlation in Figure 6 can be found here https://github.com/Ong-Research/UW_Adult_Covid-19/blob/main/04162021elisaarraycorrelationdata.xlsx.

Identifying Epitopes (Figure 7)

Requirements:

• R or RStudio
• rmarkdown package (install.packages("rmarkdown")
• UW.Adult.Covid.19 - install.packages("devtools");devtools::install("UW.Adult.Covid.19")
• Matrix - install.packages("Matrix");
• data.table - install.packages("data.table")
• multtest - https://www.bioconductor.org/packages/release/bioc/html/multtest.html
• preprocessCore - http://bioconductor.org/packages/release/bioc/html/preprocessCore.html

See find_wu1_epitopes.Rmd for other requirements.