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