differential_deviation_test — differential_deviation

Differential analysis is to test which motifs are having significant deviations among different groups. Adapted from chromVAR::differential_test

Usage

differential_deviation_test(
  deviations,
  groups = NULL,
  motifs = rownames(deviations),
  alternative = c("two.sided", "less", "greater"),
  parametric = TRUE,
  padjMethod = "BH"
)

Arguments

deviations: a data.frame contains deviations for each motif
groups: a character vector of group names or colnames(deviations)
motifs: a character vector of motif names used in analysis or rownames(deviations)
alternative: a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less".
parametric: logical, if TRUE, parametric tests are used, otherwise non-parametric tests are used.
padjMethod: method for p-value adjustment, default is "BH"

Value

a data.frame contains motifs with corresponding p-value and adjusted p-value

Examples

# Load example data
load(system.file("extdata",
    "tc_mem.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "tc_naive.rda",
    package = "methylTFR"
))
devs <- cbind(tc_mem, tc_naive)

# Construct group labels from sample names
get_groupname <- function(x) {
    return(unlist(strsplit(x, split = "_"))[1])
}
groups <- sub(".bedGraph", "", unlist(lapply(
    FUN = get_groupname,
    X = colnames(devs)
)))

# Perform differential analysis
tc_result <- differential_deviation_test(
    deviations = devs,
    groups = groups,
    motifs = rownames(devs),
    alternative = "two.sided",
    parametric = TRUE,
    padjMethod = "BH"
)