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 0.40236780 -1.14763141 -0.43601935
#> Lmo1 -0.28190038 -0.09890926 1.05152160
#> F3 -1.91920996 1.07320265 -0.56635126
#> Cnih3 -0.37425026 1.97914906 -0.08574765
#> Ppp1r3c -0.73451440 -0.01792488 1.56047701
#> Rims2 -0.13853259 0.75999353 0.08823325
#> Gfap 2.18603731 -1.75180742 1.01833281
#> Gjc3 0.38646232 -0.66634178 -0.76663924
#> Chrna4 0.43655495 0.39475675 -1.24244926
#> Prkcd -0.57035475 0.37270322 1.80315264
#> Prr18 -1.97902584 0.48687370 0.01066176
#> Grb14 0.43920644 1.20217674 0.64581753
#> Tprn 0.21566772 -1.46038692 -0.05382336
#> Clic1 -1.19619136 -1.53239558 -0.48940157
#> Olig2 1.32774402 -0.18315175 -0.74365693
#> Hrh3 1.41514297 0.41949731 -0.19542704
#> Tmbim1 0.74951127 0.47503046 -0.62226895
#> Carhsp1 -1.12524476 -1.46388165 -1.79877738
#> Tmem88b 0.69374584 -0.60716462 -2.22018550
#> Ugt8a -0.37482551 0.79407516 -1.41163658
#> Arpp19 1.76183498 0.26956404 -0.20562544
#> Lamp5 0.12558816 -0.96763874 -1.21478205
#> Galnt6 -0.59203850 0.58966838 0.88592759
#> Hlf 1.00985412 -0.52835512 0.11037987
#> Hs3st2 0.06884724 -0.22502133 0.19964012
#> Tbr1 0.54450022 0.54491887 1.20091035
#> Myl4 -0.74034508 1.30973253 -0.62971719
#> Cygb -0.74281669 -1.08679789 0.34248308
#> Ttc9b -1.38760229 0.48374155 0.71014552
#> Ipcef1 -1.37454306 -1.14758252 -0.33480466