find_highbcv_genes: Find genes with high biological coefficent of variation

Description Usage Arguments Examples

View source: R/find_highbcv_genes.R

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

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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

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