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
rankEnrich
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
#> Warning: NaNs produced
#> 30 x 3 Matrix of class "dgeMatrix"
#> cell_type1 cell_type2 cell_type3
#> Bcl11b 27 2 23
#> Lmo1 28 29 27
#> F3 13 18 18
#> Cnih3 30 17 4
#> Ppp1r3c 24 8 13
#> Rims2 1 30 30
#> Gfap 19 27 2
#> Gjc3 2 28 1
#> Chrna4 9 9 24
#> Prkcd 16 19 14
#> Prr18 3 1 26
#> Grb14 26 7 15
#> Tprn 15 12 21
#> Clic1 18 21 9
#> Olig2 14 13 20
#> Hrh3 29 3 12
#> Tmbim1 21 16 10
#> Carhsp1 4 10 29
#> Tmem88b 23 23 3
#> Ugt8a 5 6 25
#> Arpp19 22 22 5
#> Lamp5 10 24 11
#> Galnt6 17 14 17
#> Hlf 6 15 22
#> Hs3st2 11 4 28
#> Tbr1 8 25 8
#> Myl4 7 20 16
#> Cygb 20 5 19
#> Ttc9b 12 26 6
#> Ipcef1 25 11 7