R/permanovas.R

In llrs/integration-helper: Facilitate the integration

#' Permanova
#'
#' @param otus Matrix of the variables to analyze
#' @param meta Data frame with the variables to compare
#' @return An anova.cca object
permanova_otus <- function(otus, meta) {
  if (!requireNamespace("vegan", quietly = TRUE)) {
    stop("Install vegan from CRAN", call. = FALSE)
  }
  vegan::adonis(as.matrix(otus) ~ ., data = meta, method = "jaccard")
}

#' Permanova
#'
#' @param expr Matrix of the expression
#' @param meta Data frame with the variables to compare
#' @return An anova.cca object
permanova_expr <- function(expr, meta) {
  if (!requireNamespace("vegan", quietly = TRUE)) {
    stop("Install vegan from CRAN", call. = FALSE)
  }
  diss <- 1 - cor(expr)
  vegan::adonis(diss ~ ., data = meta, method = "euclidian")
}

#
# b <- adonis(as.data.frame(t(otus_table_i)) ~ AGE_SAMPLE + diagTime + AgeDiag, data = (meta_r[, nam]), method = "jaccard")
#
# > b <- adonis(t(as.matrix(otus_table_i)) ~ AGE_SAMPLE + diagTime + AgeDiag, data = as.data.frame(t(meta_r[, nam])), method = "jaccard")
# Error in eval(predvars, data, env) : object 'AGE_SAMPLE' not found