Run partial singular value decomposition using irlba
RunSVD(object, ...)
# S3 method for default
RunSVD(
object,
assay = NULL,
n = 50,
scale.embeddings = TRUE,
reduction.key = "LSI_",
scale.max = NULL,
verbose = TRUE,
irlba.work = n * 3,
tol = 1e-05,
...
)
# S3 method for Assay
RunSVD(
object,
assay = NULL,
features = NULL,
n = 50,
reduction.key = "LSI_",
scale.max = NULL,
verbose = TRUE,
...
)
# S3 method for Seurat
RunSVD(
object,
assay = NULL,
features = NULL,
n = 50,
reduction.key = "LSI_",
reduction.name = "lsi",
scale.max = NULL,
verbose = TRUE,
...
)A Seurat object
Arguments passed to other methods
Which assay to use. If NULL, use the default assay
Number of singular values to compute
Scale cell embeddings within each component to mean 0 and SD 1 (default TRUE).
Key for dimension reduction object
Clipping value for cell embeddings. Default (NULL) is no clipping.
Print messages
work parameter for irlba.
Working subspace dimension, larger values can speed convergence at the
cost of more memory use.
Tolerance (tol) parameter for irlba. Larger
values speed up convergence due to greater amount of allowed error.
Which features to use. If NULL, use variable features
Name for stored dimension reduction object. Default 'svd'
Returns a Seurat object
x <- matrix(data = rnorm(100), ncol = 10)
RunSVD(x)
#> Running SVD
#> Warning: You're computing too large a percentage of total singular values, use a standard svd instead.
#> Warning: did not converge--results might be invalid!; try increasing work or maxit
#> Scaling cell embeddings
#> Warning: No assay specified, setting assay as RNA by default.
#> Warning: Requested number is larger than the number of available items (10). Setting to 10.
#> Error in if (positive[num] == negative[num]) { negative <- negative[-num]}: argument is of length zero
RunSVD(atac_small[['peaks']])
#> Running SVD
#> Warning: You're computing too large a percentage of total singular values, use a standard svd instead.
#> Scaling cell embeddings
#> Warning: No assay specified, setting assay as RNA by default.
#> LSI_ 1
#> Positive: chr1-2157847-2188813, chr1-2471903-2481288, chr1-3815928-3820356, chr1-6843960-6846894, chr1-6051145-6055407, chr1-2515241-2519350, chr1-6659264-6664388, chr1-8935313-8940649, chr1-1549446-1552535, chr1-2343197-2348396
#> chr1-2322313-2323985, chr1-1708510-1715065, chr1-8020317-8022548, chr1-1051006-1053102, chr1-3540009-3542500, chr1-1849693-1853920, chr1-6672613-6675785, chr1-6085254-6089147, chr1-2486054-2489237, chr1-1240091-1245762
#> Negative: chr1-1532974-1533319, chr1-9153374-9153983, chr1-3759680-3759895, chr1-8685625-8685837, chr1-9161610-9161990, chr1-7975875-7976274, chr1-9143106-9143741, chr1-8469105-8469816, chr1-6651141-6652061, chr1-9239865-9240117
#> chr1-2077596-2078445, chr1-9327071-9327557, chr1-9006466-9007566, chr1-9191514-9192075, chr1-3612122-3612609, chr1-3692008-3692971, chr1-8621060-8621547, chr1-8166762-8167329, chr1-5541924-5542287, chr1-2585232-2586236
#> LSI_ 2
#> Positive: chr1-1135873-1137356, chr1-1562519-1567986, chr1-1980856-1982929, chr1-967806-970136, chr1-6523645-6526848, chr1-6507013-6510383, chr1-2573495-2575472, chr1-2454600-2456271, chr1-1140204-1144858, chr1-2227715-2234197
#> chr1-1147592-1153647, chr1-6557001-6558057, chr1-1071616-1073471, chr1-6519517-6521256, chr1-6418151-6420435, chr1-3688192-3690359, chr1-3662633-3664352, chr1-973840-977754, chr1-2756472-2757468, chr1-6295272-6296706
#> Negative: chr1-2082091-2083429, chr1-2157847-2188813, chr1-6843960-6846894, chr1-7830534-7832331, chr1-6659264-6664388, chr1-3593401-3595956, chr1-928630-937949, chr1-8000672-8003534, chr1-1695549-1696821, chr1-6639159-6642773
#> chr1-1708510-1715065, chr1-8284654-8285560, chr1-9222989-9224547, chr1-1309645-1311492, chr1-6115973-6117096, chr1-9335457-9336176, chr1-2071091-2071791, chr1-1800682-1801583, chr1-3585229-3585878, chr1-2515241-2519350
#> LSI_ 3
#> Positive: chr1-2143708-2144981, chr1-2312793-2314371, chr1-2063672-2065744, chr1-6639159-6642773, chr1-1140204-1144858, chr1-6258846-6260407, chr1-1147592-1153647, chr1-2507261-2510518, chr1-8933459-8934461, chr1-2756472-2757468
#> chr1-6483424-6485428, chr1-1788464-1789189, chr1-6761132-6762608, chr1-6613890-6615140, chr1-8186838-8187845, chr1-9064752-9065614, chr1-3540009-3542500, chr1-1849693-1853920, chr1-1057192-1058404, chr1-6500054-6501132
#> Negative: chr1-1549446-1552535, chr1-8013637-8014963, chr1-762106-763359, chr1-3773000-3774956, chr1-1333514-1336003, chr1-1207999-1210168, chr1-8584964-8586531, chr1-8008972-8009703, chr1-2486054-2489237, chr1-1562519-1567986
#> chr1-6452328-6454679, chr1-7022276-7023784, chr1-1051006-1053102, chr1-2322313-2323985, chr1-2227715-2234197, chr1-6801917-6804384, chr1-1283373-1285555, chr1-6407925-6409601, chr1-1804025-1804468, chr1-7727502-7728223
#> LSI_ 4
#> Positive: chr1-7763862-7766072, chr1-6684553-6686243, chr1-1051006-1053102, chr1-2082091-2083429, chr1-2079917-2080950, chr1-2189545-2192208, chr1-3593401-3595956, chr1-3446985-3448712, chr1-6319594-6322140, chr1-8020317-8022548
#> chr1-1306174-1308201, chr1-2507261-2510518, chr1-1509089-1511050, chr1-1333514-1336003, chr1-901313-902847, chr1-2312793-2314371, chr1-9202229-9203756, chr1-8467741-8468104, chr1-8000672-8003534, chr1-3369629-3371833
#> Negative: chr1-9188154-9190941, chr1-3806419-3808097, chr1-894021-896898, chr1-2241757-2247855, chr1-7841489-7844891, chr1-8013637-8014963, chr1-9335457-9336176, chr1-6639159-6642773, chr1-1655226-1656410, chr1-1819732-1824104
#> chr1-3815928-3820356, chr1-2125466-2127403, chr1-1341794-1343522, chr1-6304964-6307369, chr1-1562519-1567986, chr1-9293115-9295644, chr1-1597084-1597513, chr1-3565942-3569718, chr1-1397565-1398360, chr1-1839727-1841458
#> LSI_ 5
#> Positive: chr1-954372-958413, chr1-8020317-8022548, chr1-9293115-9295644, chr1-3773000-3774956, chr1-7830534-7832331, chr1-1288121-1291291, chr1-6659264-6664388, chr1-875427-878705, chr1-1839727-1841458, chr1-6085254-6089147
#> chr1-9241288-9242647, chr1-804872-805761, chr1-1788464-1789189, chr1-1002063-1006231, chr1-6268667-6270086, chr1-713460-714823, chr1-6187544-6188439, chr1-3535177-3536355, chr1-6208425-6209293, chr1-1240091-1245762
#> Negative: chr1-2486054-2489237, chr1-6258846-6260407, chr1-6639159-6642773, chr1-3712392-3713775, chr1-1057192-1058404, chr1-1446312-1448163, chr1-1259506-1261414, chr1-928630-937949, chr1-1655226-1656410, chr1-3565942-3569718
#> chr1-994056-995654, chr1-6672613-6675785, chr1-2135022-2137621, chr1-762106-763359, chr1-6051145-6055407, chr1-8762907-8763964, chr1-973840-977754, chr1-2082091-2083429, chr1-1549446-1552535, chr1-1608771-1610748
RunSVD(atac_small)
#> Running SVD
#> Warning: You're computing too large a percentage of total singular values, use a standard svd instead.
#> Scaling cell embeddings
#> An object of class Seurat
#> 1323 features across 100 samples within 3 assays
#> Active assay: peaks (323 features, 323 variable features)
#> 2 other assays present: bins, RNA
#> 2 dimensional reductions calculated: lsi, umap