Function to convert a single-cell count matrix and a corresponding single-cell cluster vector into a rank matrix that can be used with the Rank enrichment option.
makeSignMatrixRank(
sc_matrix,
sc_cluster_ids,
ties_method = c("random", "max"),
gobject = NULL
)matrix
sign_gene <- c(
"Bcl11b", "Lmo1", "F3", "Cnih3", "Ppp1r3c", "Rims2", "Gfap",
"Gjc3", "Chrna4", "Prkcd", "Prr18", "Grb14", "Tprn", "Clic1", "Olig2",
"Hrh3", "Tmbim1", "Carhsp1", "Tmem88b", "Ugt8a", "Arpp19", "Lamp5",
"Galnt6", "Hlf", "Hs3st2", "Tbr1", "Myl4", "Cygb", "Ttc9b", "Ipcef1"
)
sign_matrix <- matrix(rnorm(length(sign_gene) * 3), nrow = length(sign_gene))
rownames(sign_matrix) <- sign_gene
colnames(sign_matrix) <- c("cell_type1", "cell_type2", "cell_type3")
makeSignMatrixRank(
sc_matrix = sign_matrix,
sc_cluster_ids = c("cell_type1", "cell_type2", "cell_type3")
)
#> Warning: NaNs produced
#> 30 x 3 Matrix of class "dgeMatrix"
#> cell_type1 cell_type2 cell_type3
#> Bcl11b 7 5 30
#> Lmo1 24 11 16
#> F3 6 24 13
#> Cnih3 18 6 24
#> Ppp1r3c 1 25 28
#> Rims2 28 22 5
#> Gfap 29 2 6
#> Gjc3 22 14 10
#> Chrna4 20 7 19
#> Prkcd 4 19 25
#> Prr18 15 30 3
#> Grb14 26 8 14
#> Tprn 14 21 11
#> Clic1 16 18 15
#> Olig2 3 12 26
#> Hrh3 13 10 22
#> Tmbim1 2 9 29
#> Carhsp1 25 27 4
#> Tmem88b 23 15 9
#> Ugt8a 5 26 8
#> Arpp19 19 4 23
#> Lamp5 11 1 27
#> Galnt6 10 20 17
#> Hlf 8 16 21
#> Hs3st2 12 23 7
#> Tbr1 27 3 18
#> Myl4 21 13 12
#> Cygb 30 29 1
#> Ttc9b 17 28 2
#> Ipcef1 9 17 20