scoreEigengenes: scoreEigengenes

Description Usage Arguments

View source: R/eigengene_scoring.R

Description

scoreEigengenes

Usage

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scoreEigengenes(object, ...)

## Default S3 method:
scoreEigengenes(object, module_list, md = NULL,
  score_func = "rsvd", ...)

## S3 method for class 'DESeqDataSet'
scoreEigengenes(object, module_list,
  return_self = TRUE, score_func = "rsvd", ...)

Arguments

object

Either a matrix of expression values, a DESeqDataSet object, or a Seurat object

...

Not used

module_list

A named lists of lists where each sublist are the genes that make up the module and each sublist is named.

md

Optional meta data to add to the scores (for plotting purposes). Default: NULL

score_func

Factorization method to use in scoring. Currently only 'rsvd', 'svd', and 'nmf' are allowed. Default: 'rsvd'

return_self

return a form of 'object' with the scores added to it. Default: TRUE

assay

Seurat assay object from which to pull data

slot

Assay slot to use


milescsmith/moduleScoreR documentation built on Sept. 26, 2019, 8:38 p.m.