R/internalConstants.R

In milescsmith/WGCNA: Weighted Correlation Network Analysis

# Definitions of internal constants.

.pearsonFallbacks <- c("none", "individual", "all")
.threadAllowVar <- "ALLOW_WGCNA_THREADS"


.zeroMADWarnings <- c(
  "Some results will be NA.",
  "Pearson correlation was used for individual columns with zero (or missing) MAD.",
  "Pearson correlation was used for entire variable."
)
..minNGenes <- 4
..minNSamples <- 4
.largestBlockSize <- 1e8
.networkTypes <- c("unsigned", "signed", "signed hybrid")
.adjacencyTypes <- c(.networkTypes, "distance")
.TOMTypes <- c("none", "unsigned", "signed")
.TOMDenoms <- c("min", "mean")
.corTypes <- c("pearson", "bicor")
.corFnc <- c("cor", "bicor", "cor")
.corOptions <- c("use = 'p'", "use = 'p'", "use = 'p', method = 'spearman'")
.corOptionList <- list(list(use = "p"), list(use = "p"), list(use = "p", method = "spearman"))