groupRotations | R Documentation |
Calculates rotations based on each group Calculates rotations based on each group
groupRotations(exprData, genes, geneColName, groups, outDir, geneTransform = function(x) { mouse2human(x)$humanGene }, synonymTaxID = NULL)
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' |
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