Test for k-mer differential affinities

Source: R/kmerTestContrast.R

Using estimated k-mer level affinities returned by kmerFit, this function tests for differential affinities across conditions for each k-mer separately. The call to kmerFit must have been made with contrasts = TRUE.

While a column for the baseline condition of the contrasts is included in the returned SummarizedExperiment object to match the dimensions of the input object, all values for this column are set to NA.

After estimating k-mer level affinities using probe-set aggregate, this function tests for differential affinity between conditions.

kmerTestContrast(se)

Arguments

se

SummarizedExperiment of k-mer results from kmerFit with contrasts = TRUE.

Value

SummarizedExperiment of k-mer differential affinity results with the following assays:

  • "contrastAverage": input k-mer average affinities.

  • "contrastDifference": input k-mer differential affinities.

  • "contrastVariance": input k-mer differential affinity variances.

  • "contrastZ": studentized differences (contrastDifference / sqrt(contrastVariance)).

  • "contrastP": two-sided tail p-values for studentized differences.

  • "contrastQ": FDR-controlling Benjamini-Hochberg adjusted p-values.