calculate_ilisi: Calculate iLISI (integration Local Inverse Simpson's Index)...
In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA
View source: R/calculate_ilisi.R
calculate_ilisi R Documentation
Calculate iLISI (integration Local Inverse Simpson's Index) scores
Description
Calculate iLISI (integration Local Inverse Simpson's Index) scores
Usage
calculate_ilisi(merged_sce, pc_name, batch_column = "library_id")
Arguments
merged_sce
The merged SCE object containing data from multiple batches
pc_name
The name that allows access to the PCs. Example: fastMNN_PCA
batch_column
The variable in 'merged_sce' indicating the grouping of interest.
Generally this is either batches or cell types. Default is "library_id".
Value
Data frame with three columns, one row per cell. Columns are 'ilisi_score',
'ilisi_score_norm', 'cell_barcode', and 'batch_id'. The column 'ilisi_score_norm'
is a normalized version if 'ilisi_score' where values range from [0,1], inclusive
AlexsLemonade/scpcaTools documentation built on July 12, 2024, 8:34 a.m.
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View source: R/calculate_ilisi.R
| calculate_ilisi | R Documentation |
Calculate iLISI (integration Local Inverse Simpson's Index) scores
Description
Calculate iLISI (integration Local Inverse Simpson's Index) scores
Usage
calculate_ilisi(merged_sce, pc_name, batch_column = "library_id")
Arguments
merged_sce |
The merged SCE object containing data from multiple batches |
pc_name |
The name that allows access to the PCs. Example: fastMNN_PCA |
batch_column |
The variable in 'merged_sce' indicating the grouping of interest. Generally this is either batches or cell types. Default is "library_id". |
Value
Data frame with three columns, one row per cell. Columns are 'ilisi_score', 'ilisi_score_norm', 'cell_barcode', and 'batch_id'. The column 'ilisi_score_norm' is a normalized version if 'ilisi_score' where values range from [0,1], inclusive
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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