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