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