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