Description Usage Arguments Details Value Usage Examples References
View source: R/template_match.R
Provides scores for genes where increasing values indicate closer concordance to some pattern of interest such as genes that have monotonically increasing, decreasing, or a peak in the middle, etc. This is called "template matching" in the field, which was (I think) originally coined by Pavlidis.
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template_match( x, template = "ascending", cor_method = c("spearman", "pearson", "kendall"), ... )
A FacileAnalysis result (likely FacileAnovaAnalysisResult). We assume the formula was an intercept/effect model.
Defines the template to match against. Can be specified by
name for simple template (like
This implementation follows the main idea from the
in the MApckg package.
Analysis of strain and regional variation in gene expression in mouse brain https://doi.org/10.1186/gb-2001-2-10-research0042 (pavlidis et al.)
Gene Time Eχpression Warper: a tool for alignment, template matching and visualization of gene expression time series. https://doi.org/10.1093/bioinformatics/bti787
Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data. https://doi.org/10.1186/1471-2105-8-240
This is a bad name for this function, but just putting it down here.
a tibble of features that match the template pattern
Imagine we have several timepoints encoded in a 'group' covariate. you can run an nova to find genes that have some association w/ time, then find ones within that result that match your template (let's say ones that increase over time
increasing <- fds %>% flm_def("group") %>% fdge() %>% template_match("ascending)
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