Function to convert a single-cell RNAseq matrix into a format
that can be used with runDWLSDeconv.
makeSignMatrixDWLSfromMatrix(matrix, sign_gene, cell_type_vector)scRNA-seq matrix
genes to use (e.g. marker genes)
vector with cell types (length = ncol(matrix))
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 -0.51515610 0.1381641782 -0.362865982
#> Lmo1 -1.37271459 0.2373796845 -1.332673595
#> F3 1.30542033 1.1100917761 -0.315494009
#> Cnih3 1.10881834 0.8005185862 -0.731120481
#> Ppp1r3c -1.45820443 -0.7580063132 1.149071652
#> Rims2 -0.71320391 1.4240523360 0.682609295
#> Gfap -0.54396403 -0.0001271527 1.026893029
#> Gjc3 1.21720754 0.4183747338 -0.151021643
#> Chrna4 0.67819032 -0.1584044840 2.945098704
#> Prkcd 0.11660663 0.0828946056 -0.154675285
#> Prr18 -0.79359049 -0.4162924264 -1.336868154
#> Grb14 -1.67609289 0.4780099112 -0.581065842
#> Tprn -2.02981069 0.9405363652 0.983957313
#> Clic1 1.13508378 -0.9581794378 -1.255668221
#> Olig2 0.60121642 1.3771568736 1.535580128
#> Hrh3 -0.02335030 -0.4417146773 1.085987839
#> Tmbim1 -1.80868379 0.1637852364 0.571932231
#> Carhsp1 0.15344076 0.2588862012 -1.004001155
#> Tmem88b 0.34731639 0.0623105215 -1.457518653
#> Ugt8a -0.70172072 0.2618110014 0.890518925
#> Arpp19 -0.25676249 -0.2511373410 -0.103248088
#> Lamp5 -0.84828793 0.2579212016 -0.823708470
#> Galnt6 -1.21429581 0.3549361968 -0.114014299
#> Hlf 0.56566797 -1.0506755007 2.089053693
#> Hs3st2 -0.06277394 0.6445690156 0.002092845
#> Tbr1 0.51466908 -0.7782692772 -1.696173948
#> Myl4 1.25605537 -0.1955024096 -0.105356103
#> Cygb 1.17749260 1.2910426234 0.322027130
#> Ttc9b 0.24858431 -0.1853081126 0.095800040
#> Ipcef1 -0.61133761 -0.9279807497 -0.748998048