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This package contains functions to apply multi-threshold survival analysis on count data (e.g. microbe abundances, gene expression), using (1) survival information and (2) counts.
survivalByQuantile generates a table with cox analysis
parameters at various threshold quantile
calculateArea integrates the area above a 0.05 log
likehood p-value threshold and outputs a scalar that can be used to rank
the importance of different features
ToWide converts the count matrix reads from long format
to wide format
# Currently available as the development version on GitHub
install.packages("devtools")
devtools::install_github("spakowiczlab/mt.surv")Andersen, P. and Gill, R. (1982). Cox’s regression model for counting processes, a large sample study. Annals of Statistics 10, 1100-1120.
Therneau, T., Grambsch, P., Modeling Survival Data: Extending the Cox Model. Springer-Verlag, 2000.
submitted
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.