scoreEigengenes: scoreEigengenes

In milescsmith/moduleScoreR: Determines module scores for RNAseq data

Description

scoreEigengenes

Usage

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",
  normalize_func = c("vst", "rlog"),
  ...
)

## S3 method for class 'DGEList'
scoreEigengenes(
  object,
  module_list,
  return_self = TRUE,
  score_func = "rsvd",
  normalize_func = c("cpm", "rpkm"),
  ...
)

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

Value

DESeqDataSet with scores added to the colData

DGEList with module scores added to "samples" list component

milescsmith/moduleScoreR documentation built on Aug. 21, 2021, 3:58 a.m.