velocityInfoConos {conos}

RNA velocity analysis on samples integrated with conos Create a list of objects to pass into gene.relative.velocity.estimates function from the velocyto.R package

Description

RNA velocity analysis on samples integrated with conos Create a list of objects to pass into gene.relative.velocity.estimates function from the velocyto.R package

Usage

velocityInfoConos(
  cms.list,
  con,
  clustering = NULL,
  groups = NULL,
  n.odgenes = 2000,
  verbose = TRUE,
  min.max.cluster.average.emat = 0.2,
  min.max.cluster.average.nmat = 0.05,
  min.max.cluster.average.smat = 0.01
)

Arguments

cms.list

list of velocity files written out as cell.counts.matrices.rds files by running dropest with -V option

con

conos object (after creating an embedding and running leiden clustering)

clustering

name of clustering in the conos object to use (default=NULL). Either 'clustering' or 'groups' must be provided.

groups

set of clusters to use (default=NULL). Ignored if 'clustering' is not NULL.

n.odgenes

numeric Number of overdispersed genes to use for PCA (default=2000).

verbose

boolean Whether to use verbose mode (default=TRUE)

min.max.cluster.average.emat

Required minimum average expression count for emat, the spliced (exonic) count matrix (default=0.2). Note: no normalization is perfomed. See the parameter 'min.max.cluster.average' in the function 'filter.genes.by.cluster.expression.'

min.max.cluster.average.nmat

Required minimum average expression count for nmat, the unspliced (nascent) count matrix (default=0.05). Note: no normalization is perfomed. See the parameter 'min.max.cluster.average' in the function 'filter.genes.by.cluster.expression.'

min.max.cluster.average.smat

Required minimum average expression count for smat, the spanning read matrix (used in offset calculations) (default=0.01). Note: no normalization is perfomed. See the parameter 'min.max.cluster.average' in the function 'filter.genes.by.cluster.expression.'

Value

List with cell distances, combined spliced expression matrix, combined unspliced expression matrix, combined matrix of spanning reads, cell colors for clusters and embedding (taken from conos)