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 -1.82809337 0.6094647 0.01155014
#> Lmo1 -0.92802232 1.3793833 0.38390247
#> F3 0.08865747 -1.2447195 0.40317424
#> Cnih3 -0.33826693 -0.1478646 0.17944391
#> Ppp1r3c 1.62873751 0.1341808 -1.61682206
#> Rims2 -0.47402744 -0.9310412 -0.38783247
#> Gfap 0.72354700 0.6287824 -1.30788243
#> Gjc3 -0.57837669 -0.5829275 0.60435232
#> Chrna4 -0.07594133 0.3909346 1.05879585
#> Prkcd -2.13484251 -1.0925441 -0.29511353
#> Prr18 -1.01318158 -1.4581180 -0.17010907
#> Grb14 -1.79546577 -0.6331839 -0.81470804
#> Tprn -1.87590961 -1.0308228 0.87819400
#> Clic1 1.05718029 -0.3732522 0.31885557
#> Olig2 -0.49451892 -0.6028840 0.10820253
#> Hrh3 1.55694192 1.2082019 -0.31797722
#> Tmbim1 -0.26468830 0.6007774 1.42715658
#> Carhsp1 -0.14252191 -0.6248015 -1.17375628
#> Tmem88b 1.20521482 -1.6458737 -0.62473699
#> Ugt8a -1.72991589 0.3873096 0.43913143
#> Arpp19 1.52773083 0.7799689 -0.99236141
#> Lamp5 -0.39184058 -0.2853624 -0.01086688
#> Galnt6 0.15821292 -0.4067005 -0.11929519
#> Hlf 0.98637323 -0.4600570 0.47688994
#> Hs3st2 -2.03977194 -0.7850272 0.11406600
#> Tbr1 -0.55554346 1.8275519 -0.39212191
#> Myl4 -0.16278100 2.2894600 -1.24711540
#> Cygb -3.14345045 0.6995967 -0.34635896
#> Ttc9b 1.57392423 -2.0101668 0.06396644
#> Ipcef1 -0.60460309 2.4741636 0.02431795