groupRotations: Calculates rotations based on each group Calculates rotations...

View source: R/estimate.R

groupRotationsR Documentation

Calculates rotations based on each group Calculates rotations based on each group

Description

Calculates rotations based on each group Calculates rotations based on each group

Usage

groupRotations(exprData, genes, geneColName, groups, outDir,
  geneTransform = function(x) {     mouse2human(x)$humanGene },
  synonymTaxID = NULL)

Arguments

exprData
genes

a named list containing marker gene lists of each cell type

geneColName

character. name of the column containing the gene names in the expression file

groups

a vector stating which groups each sample belongs to

outDir

if provided group rotations will be saved there

geneTransform

a function that will be applied to the gene list. the default behavior is to change mouse genes to human genes. set to NULL to keep the genes as they are

synonymTaxID

Taxonomy identifier of the source of cell type markers. If provided, synonyms of the genes will be added as markers, not recommended since unrelated genes can share names

exprData

data.frame. Expression data. First collumns of the expression data should include gene names in the same format as the ones specified in the marker gene lists. Any other non-expression related fields must not be of type 'double'


oganm/neuroExpressoAnalysis documentation built on Aug. 24, 2022, 7:50 p.m.