Rshiny code for looking at the IMPACC data (https://www.impaccstudy.org/).
App includes the following key components:
Will load in the clinical data, DDA, DIA and targeted proteomics data. User can select some filters, normalisation and cut-off filter.
User will be given some simple statistics such as total number of proteins, and comparison of cut-off filters between the three acquisition methods.
Will give user info on the clinical data in specific. Includes standard tabular patients inclusion, clinical grouping, age distribution, sex, enrollment sites and ethnicity.
User can do some dimensionality reduction including PCA, t-SNE and UMAP. User can also generate a PVCA plot to assess effects of clinical parameters on distribution in a PCA.
Will run ANOVA, within-subject ANOVA or non-parametric ANOVA between the visit numbers. Will give some info on sample size, as well as plotting the trajectories of proteins across the visits. User can run enrichment analysis too.
This project includes many clinical variables. We developed a simple script that will run a t-test between any clinical variable of interest and plot it in a volcanoplot. Again, user can run some enrichment analysis on significant proteins.
User can generate a heatmap of specified proteins, as well as specified clinical factors for annotation.