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