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