Function to convert a list of signature genes (e.g. for cell types or processes) into a binary matrix format that can be used with the PAGE enrichment option. Each cell type or process should have a vector of cell-type or process specific genes. These vectors need to be combined into a list (sign_list). The names of the cell types or processes that are provided in the list need to be given (sign_names).
makeSignMatrixPAGE(sign_names, sign_list)vector with names for each provided gene signature
list of genes (signature)
matrix
sign_list <- list(cell_type1 = c("Bcl11b", "Lmo1", "F3", "Cnih3", "Ppp1r3c",
"Rims2", "Gfap", "Gjc3", "Chrna4", "Prkcd"),
cell_type2 = c("Prr18", "Grb14", "Tprn", "Clic1", "Olig2", "Hrh3", "Tmbim1",
"Carhsp1", "Tmem88b", "Ugt8a"),
cell_type2 = c("Arpp19", "Lamp5", "Galnt6", "Hlf", "Hs3st2", "Tbr1", "Myl4",
"Cygb", "Ttc9b","Ipcef1"))
makeSignMatrixPAGE(sign_names = c("cell_type1", "cell_type2", "cell_type3"),
sign_list = sign_list)
#> cell_type1 cell_type2 cell_type3
#> Arpp19 0 0 1
#> Bcl11b 1 0 0
#> Carhsp1 0 1 0
#> Chrna4 1 0 0
#> Clic1 0 1 0
#> Cnih3 1 0 0
#> Cygb 0 0 1
#> F3 1 0 0
#> Galnt6 0 0 1
#> Gfap 1 0 0
#> Gjc3 1 0 0
#> Grb14 0 1 0
#> Hlf 0 0 1
#> Hrh3 0 1 0
#> Hs3st2 0 0 1
#> Ipcef1 0 0 1
#> Lamp5 0 0 1
#> Lmo1 1 0 0
#> Myl4 0 0 1
#> Olig2 0 1 0
#> Ppp1r3c 1 0 0
#> Prkcd 1 0 0
#> Prr18 0 1 0
#> Rims2 1 0 0
#> Tbr1 0 0 1
#> Tmbim1 0 1 0
#> Tmem88b 0 1 0
#> Tprn 0 1 0
#> Ttc9b 0 0 1
#> Ugt8a 0 1 0