covid_multiomics_mar2022
Introduction
These files are Rmd documents and associated datasets that allow for a reproducible analysis in support of the manuscript.
data wrangling
Extensive data wrangling was required to begin analysis work.
"import_metadata.Rmd" :
- import raw metadata, filter and mutate, and write out a "masterkey" table that associates samples across data types
"import_munge_RNAseq.Rmd" :
- Read in the raw bcmatrix xls files of scaled, log-normed data, row bind into a large table, write out as one CSV for analysis
"import_munge_proteome.Rmd" :
- Read the Olink formatted xlsx data, do name fixes, filter for plasma samples, write out CSV
"import_munge_exome.Rmd" :
- Loop over TSV variant files, combine into one large data table by cohort, filter using various strategies, do data viz
sPLS-DA analysis
"mixomics_sPLS_DA_predictive_OCT2022.Rmd" :
- contains code to use mixomics sPLS-DA and DIABLO models to find correlations between RNA-seq and proteomics data
- uses the munged datasets from the data wrangling code as inputs
- performs both RNA-seq and Proteomic single datatype PLS-DA models with covid severity as the outcome (Y)
- performs integrated RNA-seq and proteomic two-way sPLS-DA (DIABLO) with covid severity as the outcome (Y)
exome analysis
- Exome analysis is currently performed in the file "import_munge_exome.Rmd".