do_lsi: do_lsi
In sankaranlab/SCAVENGE: Identifying genetic trait/phenotype relevant cell type/state at single cell resolution
do_lsi R Documentation
do_lsi
Description
Get a LSI matrix (cell-by-LSI) from TF-IDF matrix from single cell profiles
Usage
do_lsi(mat, dims = 30)
Arguments
mat
(sparse matrix) A saparse matrix of TF-IDF matrix (LSI) used for SVD
dims
number of LSIs to calculate (default:30)
Value
a sparse matrix of LSI
Examples
SE_pbmc5k <- example_data(name="pbmc5k_SE.rda")
peak_by_cell_mat <- SummarizedExperiment::assay(SE_pbmc5k)
#### Downsample to speed up example ####
peak_by_cell_mat <- peak_by_cell_mat[seq_len(500), seq_len(100)]
tfidf_mat <- tfidf(bmat=peak_by_cell_mat)
lsi_mat <- do_lsi(mat=tfidf_mat, dims=30)
sankaranlab/SCAVENGE documentation built on March 2, 2023, 2:17 a.m.
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.
| do_lsi | R Documentation |
do_lsi
Description
Get a LSI matrix (cell-by-LSI) from TF-IDF matrix from single cell profiles
Usage
do_lsi(mat, dims = 30)
Arguments
mat |
(sparse matrix) A saparse matrix of TF-IDF matrix (LSI) used for SVD |
dims |
number of LSIs to calculate (default:30) |
Value
a sparse matrix of LSI
Examples
SE_pbmc5k <- example_data(name="pbmc5k_SE.rda") peak_by_cell_mat <- SummarizedExperiment::assay(SE_pbmc5k) #### Downsample to speed up example #### peak_by_cell_mat <- peak_by_cell_mat[seq_len(500), seq_len(100)] tfidf_mat <- tfidf(bmat=peak_by_cell_mat) lsi_mat <- do_lsi(mat=tfidf_mat, dims=30)
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.