Description Usage Arguments Value Examples
View source: R/get_expressed_genes.R
get_expressed_genes() finds genes expressed in a CellDataSet object according to defined parameters.
1 2 | get_expressed_genes(cds, cell_threshold = 1, min_prop = NULL,
min_condition = NULL)
|
cds |
a CellDataSet object used in the monocle package |
cell_threshold |
numerical threshold for number of cells that must express a particular gene e.g. 1; if min_prop is specified, this number will be overridden. |
min_prop |
minimum proportion of cells that must express a particular gene e.g. 0.05 for the gene to be considered expressed |
min_condition |
a column in pData(cds) that specifies a condition e.g. genotype to which the min_prop argument will be applied; must be specified together with the min_prop argument. Takes the minimum proportion of the condition with fewer cells as the threshold for finding expressed genes. |
CellDataSet object
1 | expressed_genes <- get_expressed_genes(dat, min_prop=0.05, min_condition="genotype")
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