run.trait.association: run.trait.association

In lutsik/MeDeCom: Decomposition of heterogeneous methylomes

run.trait.association

Description

Computes test statistics for all possible group assignments of samples defined in medecom.set and rnb.set and stores heatmaps of p-values on the given location for all CG Subsets, Ks and lambdas present in medecom.set

Usage

run.trait.association(
  medecom.set,
  pheno.data,
  test.fun = t.test,
  plot.path = getwd(),
  figure.format = "pdf"
)

Arguments

medecom.set	An object of type MeDeComSet as the result of runMeDeCom containing LMCs and their proportions in the samples. The Set can contain multiple runs for different values of K and lambda.
pheno.data	An object of type RnBSet-class containing methylation data and metadata for the same samples for which medecom.set was computed or a data.frame of sample annotations (ann_S)
test.fun	Test statistic used to compute p-values of differences between LMC contributions in pairwise sample comparisons. Defaults to t.test.
plot.path	Path to store the p-value heatmaps.
figure.format	Character describing the format in which plots should be stored on disk. Either "pdf" or "png".

Details

This function creates a new folder names pdfs at the location given by plot.path and stores a heatmap for all possible Ks and lambdas defined in medecom.set. The p-values are produced by comparing the LMC contributions in all sample comparisons defined by rnb.sample.groups on rnb.set. The employed test statistic for pariwise comparison can be specified by test.fun, for groups defining more than one group kruskal.test is employed. P-values lower than 0.01 are added to the heatmap.

Author(s)

Michael Scherer

lutsik/MeDeCom documentation built on July 15, 2024, 4:51 a.m.