Description Usage Arguments Examples
View source: R/find_highbcv_genes.R
find_highbcv_genes() return genes with a high biological coefficent of variation (bcv) from a monocle CellDataSet object, subject to a number of thresholds including expression in number of cells, expression levels and residuals.
1 2 3 | find_highbcv_genes(cds, annotated_fData = NULL, scaled_matrix = NULL,
cell_threshold = 10, exprs_threshold = 0.001,
resid_threshold = 0.2)
|
cds |
a monocle CellDataSet object |
annotated_fData |
annotated fData object produced by the cellwrangler annotate_bcv() function; if NULL, parameters of bcv will be calculated from cds provided. |
scaled_matrix |
a scaled expression matrix derived from cds provided. Exprs(cds) should be divided by the colsums and multiplied by 10,000. |
cell_threshold |
threshold for expression in number of cells |
exprs_threshold |
mean expression threshold for expression levels |
resid_threshold |
threshold for residuals |
1 | find_highbcv_genes(dat)
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