mean_scale_cds: Mean scale expression of cell groups across multiple samples...
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

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.

1 2	mean_scale_cds(cds, sample_col, group, lowerDetectionLimit = 0.1, expressionFamily = VGAM::negbinomial.size())

`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