template_match: Score genes against a template of expression matching.

In facilebio/FacileIncubator: Incubator for half-baked ideas

Description

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.

Usage

template_match(
  x,
  template = "ascending",
  cor_method = c("spearman", "pearson", "kendall"),
  ...
)

Arguments

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 "ascending" or "descending"), or a numeric vector that provides the pattern, ie. c(1, 2, 3, 2, 1) for a "peak". Default "ascending".

Details

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

Value

a tibble of features that match the template pattern

Usage Examples

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)

References

https://rdrr.io/github/flajole/MApckg/man/PatternHunter.html

facilebio/FacileIncubator documentation built on Jan. 14, 2022, 4:57 a.m.