Read GMT File

Read data from a GMT file (Gene Matrix Transposed). The GMT format is commonly used to store gene sets or gene annotations.

Usage

read.gmt(gmt.file, dir = NULL, add.source = FALSE, nrows = -1)

Arguments

gmt.file

Path to GMT file.

dir

(Optional) The directory where the GMT file is located.

add.source

(optional) Include the source information in the gene sets' names.

nrows

(optional) Number of rows to read from the GMT file.

Value

A list of gene sets: each gene set is represented as a character vector of gene names.

Examples

# \donttest{
# Read GMT file (requires file to exist)
gmt_file <- system.file("extdata", "hallmarks.gmt", package = "plaid")
if (file.exists(gmt_file)) {
  gmt <- read.gmt(gmt_file)
  print(names(gmt))
  print(head(gmt[[1]]))
  
  # Read with source information
  gmt_with_source <- read.gmt(gmt_file, add.source = TRUE)
  print(head(names(gmt_with_source)))
}
#>  [1] "HALLMARK_TNFA_SIGNALING_VIA_NFKB"          
#>  [2] "HALLMARK_HYPOXIA"                          
#>  [3] "HALLMARK_CHOLESTEROL_HOMEOSTASIS"          
#>  [4] "HALLMARK_MITOTIC_SPINDLE"                  
#>  [5] "HALLMARK_WNT_BETA_CATENIN_SIGNALING"       
#>  [6] "HALLMARK_TGF_BETA_SIGNALING"               
#>  [7] "HALLMARK_IL6_JAK_STAT3_SIGNALING"          
#>  [8] "HALLMARK_DNA_REPAIR"                       
#>  [9] "HALLMARK_G2M_CHECKPOINT"                   
#> [10] "HALLMARK_APOPTOSIS"                        
#> [11] "HALLMARK_NOTCH_SIGNALING"                  
#> [12] "HALLMARK_ADIPOGENESIS"                     
#> [13] "HALLMARK_ESTROGEN_RESPONSE_EARLY"          
#> [14] "HALLMARK_ESTROGEN_RESPONSE_LATE"           
#> [15] "HALLMARK_ANDROGEN_RESPONSE"                
#> [16] "HALLMARK_MYOGENESIS"                       
#> [17] "HALLMARK_PROTEIN_SECRETION"                
#> [18] "HALLMARK_INTERFERON_ALPHA_RESPONSE"        
#> [19] "HALLMARK_INTERFERON_GAMMA_RESPONSE"        
#> [20] "HALLMARK_APICAL_JUNCTION"                  
#> [21] "HALLMARK_APICAL_SURFACE"                   
#> [22] "HALLMARK_HEDGEHOG_SIGNALING"               
#> [23] "HALLMARK_COMPLEMENT"                       
#> [24] "HALLMARK_UNFOLDED_PROTEIN_RESPONSE"        
#> [25] "HALLMARK_PI3K_AKT_MTOR_SIGNALING"          
#> [26] "HALLMARK_MTORC1_SIGNALING"                 
#> [27] "HALLMARK_E2F_TARGETS"                      
#> [28] "HALLMARK_MYC_TARGETS_V1"                   
#> [29] "HALLMARK_MYC_TARGETS_V2"                   
#> [30] "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION"
#> [31] "HALLMARK_INFLAMMATORY_RESPONSE"            
#> [32] "HALLMARK_XENOBIOTIC_METABOLISM"            
#> [33] "HALLMARK_FATTY_ACID_METABOLISM"            
#> [34] "HALLMARK_OXIDATIVE_PHOSPHORYLATION"        
#> [35] "HALLMARK_GLYCOLYSIS"                       
#> [36] "HALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY"  
#> [37] "HALLMARK_P53_PATHWAY"                      
#> [38] "HALLMARK_UV_RESPONSE_UP"                   
#> [39] "HALLMARK_UV_RESPONSE_DN"                   
#> [40] "HALLMARK_ANGIOGENESIS"                     
#> [41] "HALLMARK_HEME_METABOLISM"                  
#> [42] "HALLMARK_COAGULATION"                      
#> [43] "HALLMARK_IL2_STAT5_SIGNALING"              
#> [44] "HALLMARK_BILE_ACID_METABOLISM"             
#> [45] "HALLMARK_PEROXISOME"                       
#> [46] "HALLMARK_ALLOGRAFT_REJECTION"              
#> [47] "HALLMARK_SPERMATOGENESIS"                  
#> [48] "HALLMARK_KRAS_SIGNALING_UP"                
#> [49] "HALLMARK_KRAS_SIGNALING_DN"                
#> [50] "HALLMARK_PANCREAS_BETA_CELLS"              
#> [1] "JUNB"    "CXCL2"   "ATF3"    "NFKBIA"  "TNFAIP3" "PTGS2"  
#> [1] "HALLMARK_TNFA_SIGNALING_VIA_NFKB (http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_TNFA_SIGNALING_VIA_NFKB)"      
#> [2] "HALLMARK_HYPOXIA (http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_HYPOXIA)"                                      
#> [3] "HALLMARK_CHOLESTEROL_HOMEOSTASIS (http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_CHOLESTEROL_HOMEOSTASIS)"      
#> [4] "HALLMARK_MITOTIC_SPINDLE (http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MITOTIC_SPINDLE)"                      
#> [5] "HALLMARK_WNT_BETA_CATENIN_SIGNALING (http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_WNT_BETA_CATENIN_SIGNALING)"
#> [6] "HALLMARK_TGF_BETA_SIGNALING (http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_TGF_BETA_SIGNALING)"                
# }