Computes the mean, standard deviations, and signal-to-noise ratio (SNR)
for each element across a list of FBMs in an anglemania_object.
get_list_stats(angl)A list containing three matrices: mean_zscore,
sds_zscore, and sn_zscore.
sce <- sce_example()
angl <- create_anglemania_object(sce, batch_key = "batch")
#> No dataset_key specified.
#> Assuming that all samples belong to the same dataset and are separated by batch_key: batch
#> Extracting count matrices...
#> Filtering each batch to at least 1 cells per gene...
#> Using the intersection of filtered genes from all batches...
#> Number of genes in intersected set: 300
#>
| | 0 % elapsed=00s
|==================================================| 100% elapsed=00s, remaining~00s
angl <- anglemania(angl)
#> Computing angles and transforming to z-scores...
#>
| | 0 % elapsed=00s
|========================= | 50% elapsed=00s, remaining~00s
|==================================================| 100% elapsed=00s, remaining~00s
#> Computing statistics...
#> Weighting matrix_list...
#> Calculating mean...
#> Calculating sds...
#> Filtering features...
#> Selecting features...
#> If desired, you can re-run the selection of genes with a lower zscore_mean_threshold and/or zscore_sn_threshold by using the 'select_genes' function. e.g.: angl <- select_genes(angl, zscore_mean_threshold = 1, zscore_sn_threshold = 1, max_n_genes = 2000)
#> Please inspect get_anglemania_genes(angl)$info for info on the scores of the selected gene pairs.
#> [1] "Selected 36 genes for integration."
list_stats(angl) <- get_list_stats(angl)
#> Weighting matrix_list...
#> Calculating mean...
#> Calculating sds...
str(list_stats(angl))
#> List of 3
#> $ mean_zscore:Reference class 'FBM' [package "bigstatsr"] with 15 fields
#> ..$ extptr :<externalptr>
#> ..$ extptr_rw :<externalptr>
#> ..$ nrow : int 300
#> ..$ ncol : int 300
#> ..$ type : Named int 8
#> .. ..- attr(*, "names")= chr "double"
#> ..$ backingfile : chr "/tmp/Rtmpa1WtuS/file1d2464c13d0f.bk"
#> ..$ is_read_only: logi FALSE
#> ..$ address :<externalptr>
#> ..$ address_rw :<externalptr>
#> ..$ bk : chr "/tmp/Rtmpa1WtuS/file1d2464c13d0f.bk"
#> ..$ rds : chr "/tmp/Rtmpa1WtuS/file1d2464c13d0f.rds"
#> ..$ is_saved : logi FALSE
#> ..$ type_chr : chr "double"
#> ..$ type_size : int 8
#> ..$ file_size : num 720000
#> ..and 22 methods, of which 8 are possibly relevant:
#> .. add_columns, bm, bm.desc, check_dimensions, check_write_permissions,
#> .. initialize, save, show#envRefClass
#> $ sds_zscore :Reference class 'FBM' [package "bigstatsr"] with 15 fields
#> ..$ extptr :<externalptr>
#> ..$ extptr_rw :<externalptr>
#> ..$ nrow : int 300
#> ..$ ncol : int 300
#> ..$ type : Named int 8
#> .. ..- attr(*, "names")= chr "double"
#> ..$ backingfile : chr "/tmp/Rtmpa1WtuS/file1d241db667c9.bk"
#> ..$ is_read_only: logi FALSE
#> ..$ address :<externalptr>
#> ..$ address_rw :<externalptr>
#> ..$ bk : chr "/tmp/Rtmpa1WtuS/file1d241db667c9.bk"
#> ..$ rds : chr "/tmp/Rtmpa1WtuS/file1d241db667c9.rds"
#> ..$ is_saved : logi FALSE
#> ..$ type_chr : chr "double"
#> ..$ type_size : int 8
#> ..$ file_size : num 720000
#> ..and 22 methods, of which 8 are possibly relevant:
#> .. add_columns, bm, bm.desc, check_dimensions, check_write_permissions,
#> .. initialize, save, show#envRefClass
#> $ sn_zscore :Reference class 'FBM' [package "bigstatsr"] with 15 fields
#> ..$ extptr :<externalptr>
#> ..$ extptr_rw :<externalptr>
#> ..$ nrow : int 300
#> ..$ ncol : int 300
#> ..$ type : Named int 8
#> .. ..- attr(*, "names")= chr "double"
#> ..$ backingfile : chr "/tmp/Rtmpa1WtuS/file1d244c02d31a.bk"
#> ..$ is_read_only: logi FALSE
#> ..$ address :<externalptr>
#> ..$ address_rw :<externalptr>
#> ..$ bk : chr "/tmp/Rtmpa1WtuS/file1d244c02d31a.bk"
#> ..$ rds : chr "/tmp/Rtmpa1WtuS/file1d244c02d31a.rds"
#> ..$ is_saved : logi FALSE
#> ..$ type_chr : chr "double"
#> ..$ type_size : int 8
#> ..$ file_size : num 720000
#> ..and 22 methods, of which 8 are possibly relevant:
#> .. add_columns, bm, bm.desc, check_dimensions, check_write_permissions,
#> .. initialize, save, show#envRefClass