makeSignMatrixDWLSfromMatrix

Source: R/spatial_enrichment.R

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

runDWLSDeconv

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   0.31091163  0.20036664  0.122391764
#> Lmo1    -1.15609418  0.14503245  0.414915504
#> F3       0.87626888  1.44473499 -0.449266651
#> Cnih3    0.64519426  0.28929523  1.194585860
#> Ppp1r3c -2.45450571 -0.11746111 -0.742167598
#> Rims2    0.84690259  0.47249099 -0.477203714
#> Gfap     1.06411528  2.25476414  0.824925307
#> Gjc3    -1.27326164  0.36993922  0.055315812
#> Chrna4   0.88740813 -0.36321106  0.103634360
#> Prkcd    0.95966200  0.70079623 -1.301161158
#> Prr18   -0.45455067 -0.58631122 -0.329938782
#> Grb14   -0.85470527  0.22240216 -0.882945062
#> Tprn     1.63054980  0.73702112  1.467834929
#> Clic1    1.68814116 -0.24251998 -0.777371514
#> Olig2    2.83202325 -0.27874095 -0.125583917
#> Hrh3     0.33457433  0.65731980  0.809700370
#> Tmbim1   0.94781651  0.41060575 -0.886407775
#> Carhsp1 -0.41109244 -1.74331165 -0.210810479
#> Tmem88b -0.85649294 -0.96022345 -0.124433351
#> Ugt8a    0.86424497  0.08002093 -0.405155513
#> Arpp19  -0.52194364 -0.70651552 -1.724825822
#> Lamp5   -0.95384718 -1.20922773 -0.439286388
#> Galnt6  -0.77163539 -1.12710216  0.073506875
#> Hlf      0.17772122  1.65236949  0.875505985
#> Hs3st2  -0.04726448 -0.88368682  1.348081624
#> Tbr1    -0.20108418 -0.34526603 -0.003289201
#> Myl4     0.36974062  0.94386790 -0.997038012
#> Cygb     1.55688676 -0.79361815  0.393942482
#> Ttc9b   -0.70229174 -0.21658982 -0.457607751
#> Ipcef1   2.00125964 -1.05701235 -0.071483473