Calculate motif enrichment — motif

Calculates motif enrichment for groups of loci (usually clusters).

Usage

motif_enrichment(pwm_q, groups, threshold = 0.99, type = "relative")

Arguments

pwm_q: A matrix representing the quantile values of a position weight matrix (PWM). This should be the output of gextract_pwm.quantile.
groups: A character vector or factor specifying the groups to which each sequence belongs. Usually a clustering result.
threshold: The threshold value for considering a position in the PWM as significant. Default is 0.99.
type: The type of enrichment calculation to perform. Possible values are "relative" (default) or "absolute".

Value

A matrix representing the motif enrichment values for each group. When type = "relative", the values are the relative enrichment of the motif in the group compared the loci in all the other groups. When type = "absolute", the values are the enrichment of the motif compared to random genome.

Examples

if (FALSE) { # \dontrun{
library(misha)
gdb.init_examples()
annot <- misha.ext::gintervals.normalize(gintervals.load("annotations"), 300)
pwm_q <- gextract_pwm.quantile(
    annot,
    motifs = c("JASPAR.CDX1", "JASPAR.CDX2"),
    dist_from_edge = 100
)
pwm_q <- as.matrix(pwm_q[, c("JASPAR.CDX1.q", "JASPAR.CDX2.q")])
groups <- c("Group1", "Group1", "Group2", "Group2", "Group2", "Group3", "Group3", "Group3")

# The threshold of 0.1 is used for demonstration purposes only.
# In practice, a threshold of 0.99 is recommended.
motif_enrichment(pwm_q, groups, threshold = 0.1, type = "relative")
motif_enrichment(pwm_q, groups, threshold = 0.1, type = "absolute")
} # }