Description Usage Arguments Functions
create a BioData from an other object
Supports sqlite3 databases as used in the cellexalVR application, 10X output files and kallisto out files.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | as_BioData(dat, ...)
## S4 method for signature 'list'
as_BioData(dat)
## S4 method for signature 'matrix'
as_BioData(dat)
## S4 method for signature 'data.frame'
as_BioData(dat)
## S4 method for signature 'cellexalvrR'
as_BioData(dat)
## S4 method for signature 'Seurat'
as_BioData(dat)
## S4 method for signature 'character'
as_BioData(dat, minUMI = 100, minGexpr = NULL)
|
dat |
a sqlite database as created by the cellexalvrR::export2cellexalvr() function |
... |
source object specififc options |
minUMI |
the minimum UMI count in order to read a cell (default=100) |
minGexpr |
the minimum UMI count for a gene to be included (default NULL - translates into 1) |
as_BioData,list-method
: create a BioData::R6 object from a Rsubread result list
as_BioData,matrix-method
: convert a matrix to a BioData::R6 object
as_BioData,data.frame-method
: convert a data.frame to a BioData::R6 object
as_BioData,cellexalvrR-method
: convert a cellexalvrR object to a SingleCells::BioData::R6 object
as_BioData,Seurat-method
: convert a seurat object into a SingleCells::BioData::R6 object
as_BioData,character-method
: character path or sqlite3 database name
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