added correlation options for ModuleConnectivity

Package: hdWGCNA

Title: hdWGCNA

Version: 0.1.1.9011

Version: 0.1.1.9012

Authors@R: c(

    person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),

           comment = c(ORCID = "0000-0002-7768-4856")),

# hdWGCNA 0.1.1.9012 (2022-08-27)

## Added

- None

## Changes

- Now includes options for other types of correlations in `ModuleConnectivity`.

# hdWGCNA 0.1.1.9011 (2022-08-17)

## Added

- None

#' ModuleConnectivity

#'

#' Computes intramodular connectivity (kME) based on module eigengenes.

#' Computes eigengene-based connectivity (kME) based on module eigengenes and the

#' gene expression in selected cell populations.

#'

#' @param seurat_obj A Seurat object

#' @param group.by column in seurat_obj@meta.data containing grouping info, ie clusters or celltypes

#' @param group_name name of the group(s) in group.by to use for kME calculation

#' @param corFnc character string specifying the function to be used to calculate co-expression similarity. Defaults to bicor. Any function returning values

#' @param corOptions 	character string specifying additional arguments to be passed to the function given by corFnc. Use "use = 'p', method = 'spearman'" to obtain Spearman correlation. Use "use = 'p'" to obtain Pearson correlation.

#' @param harmonized logical determining whether to use harmonized MEs for kME calculation

#' @param assay Assay in seurat_obj containing expression information.

#' @param slot Slot in specified, default to normalized 'data' slot.

#' @param wgcna_name The name of the hdWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples

#' ModuleConnectivity(pbmc)

ModuleConnectivity <- function(

  seurat_obj,

  group.by = NULL,

  group_name = NULL,

  corFnc = 'bicor',

  corOptions = "use='p'",

  harmonized=TRUE,

  assay = NULL,

  slot = 'data',

  group.by = NULL,

  group_name = NULL,

  wgcna_name = NULL,

  ...

){

  )[genes_use,cells.use]

  datExpr <- t(as.matrix(exp_mat))

  print(dim(datExpr))

  print('running signedKME...')

  kMEs <- WGCNA::signedKME(

    datExpr,

    MEs,

    outputColumnName = "kME",

    corFnc = "bicor",

    corFnc = corFnc,

    corOptions = corOptions,

    ...

  )

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**Note:** hdWGCNA is under active development, so you will likely run into errors and small typos

if you choose to use hdWGCNA before its first stable release.

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