dot-calcKmerEnrichment: Calculate k-mer enrichment
In fmicompbio/monaLisa: Binned Motif Enrichment Analysis and Visualization

.calcKmerEnrichment

R Documentation

Calculate k-mer enrichment

Description

Given sequences, foreground/background labels and weights, calculate the enrichment of each k-mer in foreground compared to background. This function is called by calcBinnedKmerEnr() for each bin if background != "model".

The default type of test is "fisher". Alternatively, a binomial test can be used by test = "binomial". Using Fisher's exact test has the advantage that special cases such as zero background counts are handled without ad-hoc adjustments to the k-mer frequencies.

For test = "fisher", fisher.test is used with alternative = "greater", making it a one-sided test for enrichment, as is the case with the binomial test.

Usage

.calcKmerEnrichment(k, df, test = c("fisher", "binomial"), verbose = FALSE)

Arguments

`k`	Numeric scalar giving the length of k-mers to analyze.
`df`	a `DataFrame` with sequence information as returned by `.iterativeNormForKmers()`.
`test`	type of motif enrichment test to perform.
`verbose`	A logical scalar. If `TRUE`, report on progress.

Details

The function works in ZOOPS mode, which means only one or zero occurrences of a k-mer are considered per sequence. This is helpful to reduce the impact of simple sequence repeats occurring in few sequences.

Value

A data.frame containing the motifs as rows and the columns:

motifName: : the motif name
logP: : the log p-value for enrichment (natural logarithm). If test="binomial" (default), this log p-value is identical to the one returned by Homer.
sumForegroundWgtWithHits: : the weighted number of k-mer hits in foreground sequences.
sumBackgroundWgtWithHits: : the weighted number of k-mer hits in background sequences.
totalWgtForeground: : the total sum of weights of foreground sequences.
totalWgtBackground: : the total sum of weights of background sequences.