Skip to contents

Load scGate model database

Source: R/main.R
get_scGateDB.Rd

Download, update or load local version of the scGate model database. These are stored in a GitHub repository, from where you can download specific versions of the database.

Usage

get_scGateDB(
  destination = tempdir(),
  force_update = FALSE,
  version = "latest",
  branch = c("master", "dev"),
  verbose = FALSE,
  repo_url = "https://github.com/carmonalab/scGate_models"
)

Arguments

destination

Destination path for storing the DB. The default is tempdir(); if you wish to edit locally the models and link them to the current project, set this parameter to a new directory name, e.g. scGateDB

force_update

Whether to update an existing database.

version

Specify the version of the scGate_models database (e.g. 'v0.1'). By default downloads the latest available version.

branch

branch of the scGate model repository, either 'master' (default) or 'dev' for the latest models

verbose

display progress messages

repo_url

URL path to scGate model repository database

Value

A list of models, organized according to the folder structure of the database. See the examples below.

Details

Models for scGate are dataframes where each line is a signature for a given filtering level. A database of models can be downloaded using the function get_scGateDB. You may directly use the models from the database, or edit one of these models to generate your own custom gating model.

See also

scGate load_scGate_model

Examples

scGate.model.db <- get_scGateDB()
# To see a specific model, browse the list of models:
scGate.model.db$human$generic$Myeloid
#>    levels   use_as        name
#> 1  level1 positive      Immune
#> 2  level1 positive     Myeloid
#> 3  level1 positive  Macrophage
#> 4  level1 positive Neutrophils
#> 5  level1 positive         pDC
#> 6  level1 positive     MoMacDC
#> 7  level1 negative  Epithelial
#> 8  level1 negative     Stromal
#> 9  level2 positive  Macrophage
#> 10 level2 positive     Myeloid
#> 11 level2 positive     MoMacDC
#> 12 level2 positive Neutrophils
#> 13 level2 negative       Tcell
#> 14 level2 negative       Bcell
#> 15 level2 negative Plasma_cell
#> 16 level2 negative    PanBcell
#> 17 level2 negative    Lymphoid
#>                                                         signature
#> 1                     PTPRC;LAPTM5;SRGN;CXCR4;CD52;COL1A1-;RAMP2-
#> 2                                               SPI1;CD79A-;CD19-
#> 3                           APOE;APOC1;C1QA;C1QB;C1QC;CD68;FCER1G
#> 4                                             CSF3R;FCGR3B;ANXA2-
#> 5                                           IRF7;LILRA4;TCF4;GZMB
#> 6                           LYZ;CSF1R;MSR1;MAFB;CD300E;ITGAX;CD68
#> 7  SFTPB;SLPI;WFDC2;PIGR;SLC34A2;SFTA2;AGR3;ELF3;KRT18;KRT19;KRT8
#> 8     COL1A1;COL1A2;COL3A1;DCN;LUM;ACTA2;THY1;KRT18-;KRT19-;KRT8-
#> 9                           APOE;APOC1;C1QA;C1QB;C1QC;CD68;FCER1G
#> 10                                              SPI1;CD79A-;CD19-
#> 11                          LYZ;CSF1R;MSR1;MAFB;CD300E;ITGAX;CD68
#> 12                                            CSF3R;FCGR3B;ANXA2-
#> 13                                             CD3D;CD3E;CD3G;CD2
#> 14                                          MS4A1;BANK1;PAX5;CD19
#> 15                                               MZB1;DERL3;CD19-
#> 16                                                          CD79A
#> 17                                                            LCK