BuildGeneStatList | R Documentation |
This function takes a Seurat
or SingleCellExperiment
object and
builds a list of dataframes containing gene expression statistics for all
genes of each cluster. This can be used as the input to
BuildCCInx
for generating cell-cell interaction predictions
between cell-type clusters.
BuildGeneStatList( inD, cl, assayType = "", assaySlot = "", exponent = 2, pseudocount = 1 )
inD |
The input dataset. An object of class |
cl |
a factor where each value is the cluster assignment for a cell (column) in the input gene expression matrix. |
assayType |
Default = "" (for Seurat v1/2). A length-one character
vector representing the assay slot in which the expression data is stored
in the input object. This is not required for Seurat v1 or v2 objects. See
|
assaySlot |
An optional length-one character vector representing
the slot of the Seurat v3 |
exponent |
Default = 2. A length-one numeric vector representing the
base of the log-normalized gene expression data to be processed. Generally
gene expression data is transformed into log2 space when normalizing (set
this to 2), though |
pseudocount |
Default = 1. A length-one numeric vector representing the pseudocount added to all log-normalized values in your input data. Most methods use a pseudocount of 1 to eliminate log(0) errors. |
Mean gene expression calculations Innes BT and Bader GD. scClustViz – Single-cell RNAseq cluster assessment and visualization [version 2; peer review: 2 approved]. F1000Research 2019, 7:1522 (https://doi.org/10.12688/f1000research.16198.2)
CalcCGS
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