Run GLMPCA (generalized version of principal components analysis)

Usage

RunGLMPCA(object, ...)

# S3 method for Seurat
RunGLMPCA(
  object,
  assay = NULL,
  slot = "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 Assay
RunGLMPCA(
  object,
  assay = NULL,
  slot = "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 default
RunGLMPCA(
  object,
  assay = NULL,
  slot = "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 function.
assay: A character string specifying the assay to be used for the analysis. Default is NULL.
slot: A character string specifying the slot name 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)
#> GLMPC_ 1 
#> Positive:  Dusp2, Rgs13, Ctss, Trmo, Ccl2, Rasd2, Tnni3, Isy1, Casp12, Ms4a15 
#> 	   Cmah, Cd53, Gm29155, Adamts2, Ctgf, Hpdl, AW112010, Pxdc1, Hist1h2ap, Ublcp1 
#> 	   Hist1h2an, Ddr2, AB124611, Upk3b, Cxcr4, Gp2, Gm5786, Obscn, Fcrls, Sparcl1 
#> Negative:  Bgn, Cyp4f17, Hoxb4, Nrk, Ngfr, Adgrb1, Ngf, Tspan11, Saa3, Ptchd1 
#> 	   9130230L23Rik, Fibcd1, Krtap31-1, Pgm5, Sh2d5, Scn1b, 1700128E19Rik, Gm17552, Hoxc5, Kcnc1 
#> 	   Tgm7, Dgkb, Bhlhe22, Nhlh1, Rogdi, Cd248, Avpr1b, Depdc1b, Cbln4, Kdr 
#> GLMPC_ 2 
#> Positive:  Mthfd1l, Ssu2, Dkk2, Lrrc17, Cd300lf, Prdm8, Casp1, Gp9, Fxyd5, Kpna7 
#> 	   Ctrl, Clec3b, Krtap31-1, Dusp2, Pid1, Kcng2, Lpl, Col1a2, Lrp1b, Ublcp1 
#> 	   Krtap3-2, Srpx, AI849053, AW112010, Rgs13, Pcdh18, Gad2, F13a1, Il16, Nid1 
#> Negative:  Hhip, Piezo2, Cfap100, Zcchc24, Anxa1, Depdc1b, Fam64a, Rasgrp2, Gm44296, Cenpf 
#> 	   Hist1h2ah, Parpbp, Ccnb1, Troap, Kif14, Kif2c, Ube2c, Mpeg1, Hmmr, Ascl1 
#> 	   Pif1, Slc4a1, Gm26733, Cdc20, Tpx2, Hapln3, Cenpa, Clic3, Cenpe, Kif18b 
#> GLMPC_ 3 
#> Positive:  Cxcl1, Ccl2, Pdcd1, Tnf, Cxcl2, Gpr153, Usp44, Cd4, Csf2rb, Fxyd5 
#> 	   Gp9, Adamts2, Sparcl1, Cxcl10, Krtap31-1, Gad2, F13a1, Rgs13, Prdm8, Siglech 
#> 	   Phf21b, Hes5, Gp2, Gm5786, Il16, Gm26839, Trem2, Lrp1b, Hist1h2ao, Lpl 
#> Negative:  Pde3a, Apbb1ip, Sst, Slamf9, Itga8, Ddr2, Toe1, Prnp, Irx3, Entpd8 
#> 	   Medag, Cxcl13, Ltf, Stab2, A930011G23Rik, Col1a1, Wnt6, Ptgs2, Kng2, Cpa3 
#> 	   Gpr6, Aoc1, Slco1a6, Itgb7, Col6a1, Ublcp1, Cldn5, Spock1, Gm2109, Ppy 
#> GLMPC_ 4 
#> Positive:  Pcdh18, Cd37, R3hdml, Nid1, Krtap3-2, AI849053, Ghrl, Lypd8, Cpa4, Stmn4 
#> 	   Irs4, Wnt6, Mmp2, Cxcl13, Ltf, Car14, Guca2a, H2-Ab1, Barx1, Fli1 
#> 	   Hist1h4f, Gm3839, Ccl3, Car3, Arap3, Fabp1, Arsi, Kdr, Sds, Serpina1a 
#> Negative:  Fcrls, Ms4a6d, Gna15, Cxcl1, Sparcl1, Gfra2, Ins1, RP24-143K11.1, Pde7b, Trh 
#> 	   Ptprz1, Prl, Npy, Grid1, Aif1, Tmem215, Tnfaip8l2, Ins2, Ecel1, Gm20635 
#> 	   Gip, Cxcl2, Troap, Ltc4s, Slc19a1, Tnf, Apobec1, Aldh1a3, Plat, Gm36937 
#> GLMPC_ 5 
#> Positive:  Cd36, Calcr, Fermt3, Gprasp1, Il1b, Luzp2, Lst1, Galnt13, Hoxb2, Cadm3 
#> 	   Add2, Gast, Dock2, Chil1, Asb4, Ifit3, Gabrg2, Gnb4, Mc4r, Ecm1 
#> 	   Nell1, Nrsn1, Dcn, Slc14a2, Sema6d, Islr, Hist1h3g, 4930455G09Rik, Slc18a2, Cd83 
#> Negative:  Stmn4, Krtap31-1, Cfap100, Itgal, Zcchc24, Mmp2, Hist1h2ah, Piezo2, Cd37, Siglech 
#> 	   Hhip, Fhl3, Irx3, Ccr1, Depdc1b, Phf21b, Apoe, Hoxb4, Aoc1, Sds 
#> 	   Col1a1, Tcte3, Gna15, Hapln3, Anxa1, Hist1h2an, Cxcl13, Ltf, Trem2, Gm26839 
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "glmpca")