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Load a single scGate model

Source: R/main.R
load_scGate_model.Rd

Loads a custom scGate model into R. For the format of these models, have a look or edit one of the default models obtained with get_scGateDB

Usage

load_scGate_model(model_file, master.table = "master_table.tsv")

Arguments

model_file

scGate model file, in .tsv format.

master.table

File name of the master table (in repo_path folder) that contains cell type signatures.

Value

A scGate model in dataframe format, which can given as input to the scGate function.

See also

scGate get_scGateDB

Examples

dir <- tempdir() # this may also be set to your working directory
models <- get_scGateDB(destination=dir)
#> Using local version of repo scGate_models-master. If you want update it, set option force_update = TRUE
# Original or edited model
model.path <- paste0(dir,"/scGate_models-master/human/generic/Bcell_scGate_Model.tsv")
master.path <- paste0(dir,"/scGate_models-master/human/generic/master_table.tsv")
my.model <- load_scGate_model(model.path, master.path)
my.model
#>    levels   use_as        name
#> 1  level1 positive      Immune
#> 2  level1 positive    Lymphoid
#> 3  level1 positive    PanBcell
#> 4  level1 positive       Bcell
#> 5  level1 positive         APC
#> 6  level1 negative  Epithelial
#> 7  level1 negative     Stromal
#> 8  level2 positive    Lymphoid
#> 9  level2 positive       Bcell
#> 10 level2 positive    PanBcell
#> 11 level2 negative     Myeloid
#> 12 level2 negative     MoMacDC
#> 13 level2 negative Neutrophils
#> 14 level3 positive    PanBcell
#> 15 level3 positive       Bcell
#> 16 level3 negative       Tcell
#> 17 level3 negative          NK
#> 18 level4 positive       Bcell
#>                                                               signature
#> 1                           PTPRC;LAPTM5;SRGN;CXCR4;CD52;COL1A1-;RAMP2-
#> 2                                                                   LCK
#> 3                                                                 CD79A
#> 4                                                 MS4A1;BANK1;PAX5;CD19
#> 5  HLA-DRA;HLA-DMB;HLA-DMA;HLA-DQA1;HLA-DQB1;HLA-DRB1;HLA-DPA1;HLA-DPB1
#> 6        SFTPB;SLPI;WFDC2;PIGR;SLC34A2;SFTA2;AGR3;ELF3;KRT18;KRT19;KRT8
#> 7           COL1A1;COL1A2;COL3A1;DCN;LUM;ACTA2;THY1;KRT18-;KRT19-;KRT8-
#> 8                                                                   LCK
#> 9                                                 MS4A1;BANK1;PAX5;CD19
#> 10                                                                CD79A
#> 11                                                    SPI1;CD79A-;CD19-
#> 12                                LYZ;CSF1R;MSR1;MAFB;CD300E;ITGAX;CD68
#> 13                                                  CSF3R;FCGR3B;ANXA2-
#> 14                                                                CD79A
#> 15                                                MS4A1;BANK1;PAX5;CD19
#> 16                                                   CD3D;CD3E;CD3G;CD2
#> 17                 KLRD1;NKG7;NCR1;FCGR3A;CD3D-;CD3E-;CD3G-;CD8A-;CD8B-
#> 18                                                MS4A1;BANK1;PAX5;CD19