mean_scale_cds: Mean scale expression of cell groups across multiple samples...

Description Usage Arguments Value Examples

Description

mean_scale_cds() scales the expression of cell groups e.g. CellType across multiple samples in a monocle CellDataSet object such that cells from the same cell group in every sample have the same mean expression. Assuming cells in same cell group have similar variances aross all samples, this will allow cells from the same cell group in every sample to have similar distributions.

Usage

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mean_scale_cds(cds, sample_col, group, lowerDetectionLimit = 0.1,
  expressionFamily = VGAM::negbinomial.size())

Arguments

cds

monocle CellDataSet object

sample_col

name of column in pData(cds) that annotates samples that cells are from

group

name of column in pData(cds) that annotates groups that cells are in.

lowerDetectionLimit

the minimum expression level that consistitutes true expression

expressionFamily

the VGAM family function to be used for expression response variables

Value

A CellDataSet object

Examples

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dat <- mean_scale_cds(dat0, sample_col="sample", group="CellType")

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