Function to convert a single-cell RNAseq matrix into a format
that can be used with runDWLSDeconv.
makeSignMatrixDWLSfromMatrix(matrix, sign_gene, cell_type_vector)matrix
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")
makeSignMatrixDWLSfromMatrix(
matrix = sign_matrix, sign_gene = sign_gene,
cell_type_vector = c("cell_type1", "cell_type2", "cell_type3")
)
#> cell_type1 cell_type2 cell_type3
#> Bcl11b -1.0718209 -0.4065751 -0.86399930
#> Lmo1 0.9238782 1.1723238 -1.56123143
#> F3 0.7311501 1.9259123 -2.60502767
#> Cnih3 1.7851232 -0.1823952 -0.89602760
#> Ppp1r3c 0.2261871 2.4347812 0.37904974
#> Rims2 0.5968079 -0.6353048 -0.05654510
#> Gfap -0.1652537 -0.2454793 -0.85722358
#> Gjc3 1.2956083 0.6950644 0.77741308
#> Chrna4 -1.0582362 0.8070896 -0.72886697
#> Prkcd 0.3253130 1.8357330 -0.72834256
#> Prr18 -0.8796780 0.4747621 1.42350263
#> Grb14 0.7790034 -1.1351837 0.39383048
#> Tprn 0.4977836 1.2868012 2.57381915
#> Clic1 0.1913683 -0.5414757 -0.07325674
#> Olig2 0.3591223 0.3102250 0.19861549
#> Hrh3 0.2126628 1.9217255 0.07315018
#> Tmbim1 0.1260228 -0.8088575 1.78995977
#> Carhsp1 -0.2178639 1.6546419 -0.62846818
#> Tmem88b -0.2527933 1.0831838 0.33255008
#> Ugt8a 0.9264100 1.4197332 -0.48949742
#> Arpp19 -1.4748461 0.6012553 1.44609771
#> Lamp5 1.6912880 0.5714559 0.13025587
#> Galnt6 -0.2860043 0.7154091 -0.19339160
#> Hlf 1.6092566 0.8245800 -0.16157106
#> Hs3st2 0.4521826 1.4760825 1.13307362
#> Tbr1 0.3974316 -0.2078706 0.93740154
#> Myl4 0.1869443 -1.7721229 -0.86782899
#> Cygb 0.2199893 -1.2015833 0.84200865
#> Ttc9b 1.2135576 1.5249238 0.99936801
#> Ipcef1 -1.5639109 -1.0943758 0.08910988