Run GLMPCA (generalized version of principal components analysis)

Usage

RunGLMPCA(object, ...)

# S3 method for class 'Seurat'
RunGLMPCA(
  object,
  assay = NULL,
  layer = "counts",
  features = NULL,
  L = 5,
  fam = c("poi", "nb", "nb2", "binom", "mult", "bern"),
  rev.gmlpca = FALSE,
  ndims.print = 1:5,
  nfeatures.print = 30,
  reduction.name = "glmpca",
  reduction.key = "GLMPC_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

# S3 method for class 'Assay'
RunGLMPCA(
  object,
  assay = NULL,
  layer = "counts",
  features = NULL,
  L = 5,
  fam = c("poi", "nb", "nb2", "binom", "mult", "bern"),
  rev.gmlpca = FALSE,
  ndims.print = 1:5,
  nfeatures.print = 30,
  reduction.key = "GLMPC_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

# S3 method for class 'Assay5'
RunGLMPCA(
  object,
  assay = NULL,
  layer = "counts",
  features = NULL,
  L = 5,
  fam = c("poi", "nb", "nb2", "binom", "mult", "bern"),
  rev.gmlpca = FALSE,
  ndims.print = 1:5,
  nfeatures.print = 30,
  reduction.key = "GLMPC_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

# Default S3 method
RunGLMPCA(
  object,
  assay = NULL,
  layer = "counts",
  features = NULL,
  L = 5,
  fam = c("poi", "nb", "nb2", "binom", "mult", "bern"),
  rev.gmlpca = FALSE,
  ndims.print = 1:5,
  nfeatures.print = 30,
  reduction.key = "GLMPC_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

Arguments

object: An object. This can be a Seurat object, an assay object, or a matrix-like object.
...: Additional arguments to be passed to the glmpca::glmpca function.
assay: A character string specifying the assay to be used for the analysis. Default is NULL.
layer: A character string specifying the layer to be used for the analysis. Default is "counts".
features: A character vector specifying the features to be used for the analysis. Default is NULL, which uses all variable features.
L: An integer specifying the number of components to be computed. Default is 5.
fam: A character string specifying the family of the generalized linear model to be used. Currently supported values are "poi", "nb", "nb2", "binom", "mult", and "bern". Default is "poi".
rev.gmlpca: A logical value indicating whether to perform reverse GLMPCA (i.e., transpose the input matrix) before running the analysis. Default is FALSE.
ndims.print: An integer vector specifying the dimensions (number of components) to print in the output. Default is 1:5.
nfeatures.print: An integer specifying the number of features to print in the output. Default is 30.
reduction.name: A character string specifying the name of the reduction to be stored in the Seurat object. Default is "glmpca".
reduction.key: A character string specifying the prefix for the column names of the basis vectors. Default is "GLMPC_".
verbose: A logical value indicating whether to print verbose output. Default is TRUE.
seed.use: An integer specifying the random seed to be used. Default is 11.

Examples

pancreas_sub <- RunGLMPCA(object = pancreas_sub)
#> ℹ [2025-07-26 07:51:57] GLMPC_ 1 
#> ℹ [2025-07-26 07:51:57] Positive:  Sparcl1, Crabp1, Col1a1, Col5a1, Colec12, Xkr5, Islr, Pmp22, Col1a2, Platr22 
#> ℹ [2025-07-26 07:51:57] 	   Plscr2, Ugt2b5, Trabd2b, Slc26a3, Nat8l, Tmem119, Gm6878, Spaca7, Gm7854, Ctgf 
#> ℹ [2025-07-26 07:51:57] 	   Wnt5a, Ptgfr, Tpm2, Spp2, Hhip, Gm20649, Nkain4, Slc25a48, Hist1h2an, Wdr72 
#> ℹ [2025-07-26 07:51:57] Negative:  RP23-477O13.1, Npy1r, Areg, Slc6a19, RP23-428N8.3, Gast, Nkx6-3, Myl7, Unc13d, Rbm11 
#> ℹ [2025-07-26 07:51:57] 	   Wif1, Xkr6, Bcas1os1, Tnfaip8l3, Col14a1, March11, Pyy, Oxtr, Slc25a43, Otc 
#> ℹ [2025-07-26 07:51:57] 	   Pnoc, Ccl28, Sez6l, Smim18, Pcdh8, Ptprt, Asb4, Msx1, Ppp2r2c, Skap1 
#> ℹ [2025-07-26 07:51:57] GLMPC_ 2 
#> ℹ [2025-07-26 07:51:57] Positive:  Calca, Gast, Pnoc, Col19a1, Gm12689, Mstn, P2ry12, Gm13075, Rpp25, Ins1 
#> ℹ [2025-07-26 07:51:57] 	   Rasl11a, A630076J17Rik, Meikin, Nrcam, Gpr179, Car3, Mb, Cbln4, Gcg, Pgr 
#> ℹ [2025-07-26 07:51:57] 	   Nat8l, Plscr2, Foxd3, Ngf, Ptgfr, Ctgf, Gm43948, Slc25a48, Pmp22, Xkr5 
#> ℹ [2025-07-26 07:51:57] Negative:  Unc13d, Adra2c, 4932438H23Rik, Bhlhe22, Pdcd1, Slc4a1, Snai1, Cmklr1, Ppp1r16b, Pou3f1 
#> ℹ [2025-07-26 07:51:57] 	   Fam71b, Notum, Wnt3, Tgm7, Necab3, 1700128E19Rik, Eya2, Fgf18, Aldob, Siglece 
#> ℹ [2025-07-26 07:51:57] 	   Tmem114, Myl2, Sftpc, 1520401A03Rik, Jakmip3, Epb42, Sema3g, Neurod2, Krt15, Megf11 
#> ℹ [2025-07-26 07:51:57] GLMPC_ 3 
#> ℹ [2025-07-26 07:51:57] Positive:  Wnt6, Gcg, Calcr, Agmo, Cxcl15, Sprr1a, Gm13075, 1700028P14Rik, Il17b, Oasl2 
#> ℹ [2025-07-26 07:51:57] 	   Car3, Pou6f2, Col19a1, Dpep2, Necab3, Crabp1, Hoxb2, RP23-477O13.1, Cd36, Lrrn3 
#> ℹ [2025-07-26 07:51:57] 	   Gpr179, Nrl, Rgs4, Spp2, Ppp1r3b, Vipr1, Fmod, Irx1, Calb1, Fut1 
#> ℹ [2025-07-26 07:51:57] Negative:  Thsd7a, Gm12689, Npy, Hvcn1, Htr1d, Ins2, Syndig1l, Mxd3, Pif1, Esco2 
#> ℹ [2025-07-26 07:51:57] 	   Gip, Tmem215, Rpp25, Kif11, Esyt3, Chrna3, Msx1, Ugt2b5, Casc5, Cd177 
#> ℹ [2025-07-26 07:51:57] 	   Hist1h1b, Areg, Derl3, Aurkb, Nnat, Neil3, Ncapg, Kif14, Cdkn2c, Ndc80 
#> ℹ [2025-07-26 07:51:57] GLMPC_ 4 
#> ℹ [2025-07-26 07:51:57] Positive:  Dpep2, Cxcl15, Lrrk1, Rasl11a, Gm13375, Cxcl10, Vsig8, Cxcl16, Ptpn5, Ccl20 
#> ℹ [2025-07-26 07:51:57] 	   Adm2, Slc1a4, Akr1c18, Dab2, Pgr, Fhl1, Gm13075, Thbs1, Cypt3, Clca3a2 
#> ℹ [2025-07-26 07:51:57] 	   Krt23, Tnf, Hs6st2, Creb5, Trpc4, Arhgap22, Nrarp, AU021092, Nrcam, Samd4 
#> ℹ [2025-07-26 07:51:57] Negative:  Sparcl1, Sst, Col19a1, Vipr1, 1700028P14Rik, Islr, Col1a2, Col1a1, Crabp1, Tmem119 
#> ℹ [2025-07-26 07:51:57] 	   Oxtr, Gm7854, Hhip, Il17b, Ppp1r27, Col6a1, Nkain4, Col5a1, Pgc, Cntn1 
#> ℹ [2025-07-26 07:51:57] 	   Hist1h2an, Abcc9, Slc4a1, Colec12, Gm6878, Ugt2b5, Gsg1l, Gm11789, Gcg, Ajap1 
#> ℹ [2025-07-26 07:51:57] GLMPC_ 5 
#> ℹ [2025-07-26 07:51:57] Positive:  Ghrl, Foxd3, Cbln4, Ngf, Tmem119, Irs4, Abcc9, R3hdml, Wnt6, Lrrtm3 
#> ℹ [2025-07-26 07:51:57] 	   Cym, Zcchc12, Arhgap22, Mboat4, Guca2a, Nkx6-3, Car3, Ugt2b5, Fam111a, Tox2 
#> ℹ [2025-07-26 07:51:57] 	   Elfn1, Thsd7a, Pgc, Clspn, Gm12689, St8sia2, 1700028P14Rik, Slfn9, Mcm10, Fam124a 
#> ℹ [2025-07-26 07:51:57] Negative:  3830403N18Rik, Pappa, Sprr1a, Hhip, Fndc1, Nrl, Gm26652, Aldob, Dpep2, Tmem252 
#> ℹ [2025-07-26 07:51:57] 	   Abhd11os, 2410021H03Rik, Iapp, Bcas3os2, Col19a1, Unc13d, Gp9, Oprk1, Gm11789, Zfp433 
#> ℹ [2025-07-26 07:51:57] 	   Lyve1, Slc30a8, C2cd4a, Lce6a, Ppp1r27, P2ry12, Crhr2, Elfn2, D7Ertd443e, Gm2694 
CellDimPlot(
  pancreas_sub,
  group.by = "CellType",
  reduction = "glmpca"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.