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 -1.99843344 0.27818108 0.538925791
#> Lmo1 0.79968424 -1.48070267 -2.423133101
#> F3 0.06866016 -0.46287736 0.208927567
#> Cnih3 -0.30803903 1.92692688 0.742882562
#> Ppp1r3c 0.71386479 0.29898916 0.261874114
#> Rims2 -0.29014298 0.69446539 -1.014462331
#> Gfap 0.27870986 -0.82859781 3.165906417
#> Gjc3 -0.66611380 -1.96983728 -2.220897864
#> Chrna4 -1.16856256 -1.46363099 0.706321426
#> Prkcd 1.49004958 0.51833303 -0.713366039
#> Prr18 -0.88544651 -0.63951653 0.114430178
#> Grb14 0.57355458 -0.56371054 1.546379354
#> Tprn -0.12988125 0.50064625 -1.180491672
#> Clic1 0.13818011 0.77303082 -0.189692431
#> Olig2 0.03912236 -0.05685780 0.221436012
#> Hrh3 0.45732717 0.39256061 -0.387465949
#> Tmbim1 -1.68196131 0.93609436 0.886789712
#> Carhsp1 1.42660126 -1.88565333 -2.007619970
#> Tmem88b -0.52968397 -0.85992672 -0.007769513
#> Ugt8a 1.26078314 0.02163123 -0.234023133
#> Arpp19 -0.67044898 1.17568753 0.558736658
#> Lamp5 1.29447923 0.30336215 -0.566646775
#> Galnt6 0.38567420 0.35247676 -0.597994702
#> Hlf -0.19662941 1.65162094 0.229090291
#> Hs3st2 1.39803932 -0.87284027 0.116414760
#> Tbr1 -1.09396555 -2.10039004 0.485777214
#> Myl4 0.17695276 -2.08460533 -0.251071075
#> Cygb 0.34402059 -0.43970714 -0.111357388
#> Ttc9b 1.97273596 -1.54719659 0.109337283
#> Ipcef1 0.05707011 0.40825666 1.072446804