find_highbcv_genes: Find genes with high biological coefficent of variation

In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description

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.

Usage

find_highbcv_genes(cds, annotated_fData = NULL, scaled_matrix = NULL,
  cell_threshold = 10, exprs_threshold = 0.001,
  resid_threshold = 0.2)

Arguments

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

Examples

find_highbcv_genes(dat)

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.