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