log_normalize_cds: Normalize and log monocle cds

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

Description

log_normalize_cds() globally scales and log-transforms the expression matrix of a monocle CellDataSet object. The total count for each cell (represented by a column) is scaled to have the same total as all other cells (columns). A monocle cds with the log-normalized expression matrix is returned.

Usage

log_normalize_cds(cds, filter_zeros = TRUE, scale_to = "median",
  logbase = 10)

Arguments

cds	a monocle CellDataSet object
filter_zeros	logical - if genes with zero expression should be removed; defaults to TRUE
scale_to	what value total read counts for each cell should be scaled to; by default, each cell's total count is scaled to the median of all cells' totals; a numeric value can also be specified
logbase	base for logarithm; defaults to 10; if NULL, no logarithm will be computed and the original expression matrix will be returned

Value

a monocle CellDataSet object

Examples

dat_log <- log_normalize_cds(dat, scale_to = 10000, logbase=10)

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