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.
1 2 3 4 5 6 | template_match(
x,
template = "ascending",
cor_method = c("spearman", "pearson", "kendall"),
...
)
|
x |
A FacileAnalysis result (likely FacileAnovaAnalysisResult). We assume the formula was an intercept/effect model. |
template |
Defines the template to match against. Can be specified by
name for simple template (like |
This implementation follows the main idea from the PatternHunger
function
in the MApckg package.
Other resources:
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.
GOTO: FacileAnalysis
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)
https://rdrr.io/github/flajole/MApckg/man/PatternHunter.html
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