Function to convert a single-cell RNAseq matrix into a format that can be used with runDWLSDeconv.

makeSignMatrixDWLSfromMatrix(matrix, sign_gene, cell_type_vector)

Arguments

matrix

scRNA-seq matrix

sign_gene

genes to use (e.g. marker genes)

cell_type_vector

vector with cell types (length = ncol(matrix))

Value

matrix

See also

Examples

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   1.068182066 -0.13853259  0.75999353
#> Lmo1     2.361464621  2.18603731 -1.75180742
#> F3      -0.785996165  0.38646232 -0.66634178
#> Cnih3    1.729333444  0.43655495  0.39475675
#> Ppp1r3c -1.694198249 -0.57035475  0.37270322
#> Rims2    1.141383501 -1.97902584  0.48687370
#> Gfap     0.726879505  0.43920644  1.20217674
#> Gjc3     0.029480109  0.21566772 -1.46038692
#> Chrna4   0.546886539 -1.19619136 -1.53239558
#> Prkcd    0.479983754  1.32774402 -0.18315175
#> Prr18    0.005258809  1.41514297  0.41949731
#> Grb14    0.110917364  0.74951127  0.47503046
#> Tprn     1.142474742 -1.12524476 -1.46388165
#> Clic1    1.719383004  0.69374584 -0.60716462
#> Olig2   -0.688176101 -0.37482551  0.79407516
#> Hrh3     0.953801506  1.76183498  0.26956404
#> Tmbim1   0.966492680  0.12558816 -0.96763874
#> Carhsp1  1.371811955 -0.59203850  0.58966838
#> Tmem88b -0.377596485  1.00985412 -0.52835512
#> Ugt8a    1.158070869  0.06884724 -0.22502133
#> Arpp19  -0.026400040  0.54450022  0.54491887
#> Lamp5    0.553371247 -0.74034508  1.30973253
#> Galnt6  -0.037302501 -0.74281669 -1.08679789
#> Hlf     -0.877947238 -1.38760229  0.48374155
#> Hs3st2  -0.998671076 -1.37454306 -1.14758252
#> Tbr1     0.402367799 -1.14763141 -0.43601935
#> Myl4    -0.281900377 -0.09890926  1.05152160
#> Cygb    -1.919209956  1.07320265 -0.56635126
#> Ttc9b   -0.374250265  1.97914906 -0.08574765
#> Ipcef1  -0.734514398 -0.01792488  1.56047701