Replace "." with "_" in function names

[bschilder]

Using "." in function names is generally not good coding practice as it can cause problems in some cases (e.g. exporting functions from R to python via rpy2).

[bschilder]

For each of the renamed functions, I will add a deprecation notice if the old name is used, and automatically redirect to the new function.

For example:

calculate.celltype.enrichment.probabilities.wtLimma <- function(
    magmaAdjZ,
    ctd,
    thresh = 0.0001,
    sctSpecies = "mouse",
    annotLevel = 1,
    celltypes = NULL,
    return_all = FALSE,
    verbose = TRUE){
    .Deprecated("calculate_celltype_enrichment_probabilities_wtLimma")
    calculate_celltype_enrichment_probabilities_wtLimma(
        magmaAdjZ = magmaAdjZ,
        ctd = ctd,
        thresh = thresh,
        sctSpecies = sctSpecies,
        annotLevel = annotLevel,
        celltypes = celltypes,
        return_all = return_all,
        verbose = verbose
    )
}