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  -1.8238382  0.61704482  1.22553453
#> Lmo1    -0.1349218 -0.69131863  0.20173921
#> F3      -0.7959346 -0.99288074 -0.46447342
#> Cnih3    0.4281197 -0.99967681 -2.04136387
#> Ppp1r3c  1.2039203  0.35993496  0.71876924
#> Rims2    1.6401921 -1.29307696 -1.51673819
#> Gfap     1.8171074 -1.20099430  0.47282530
#> Gjc3     0.1629464  0.68692357  1.36536590
#> Chrna4   0.8093333 -0.08618519 -0.08165745
#> Prkcd   -0.1641177  1.23291124 -0.03101319
#> Prr18    0.4821334  0.66117954  0.83201844
#> Grb14    1.3028753 -0.60756312 -0.77213576
#> Tprn    -1.3830808  0.81815801 -0.76483617
#> Clic1   -1.3328310  0.47074487 -0.12474830
#> Olig2   -2.1522721 -0.56739305 -0.23013025
#> Hrh3     0.3595989 -0.64760874 -0.68304060
#> Tmbim1  -0.7120629  1.18755929 -1.66018744
#> Carhsp1  0.7595427  1.29613370  1.94457303
#> Tmem88b -0.3048478  0.80475188 -1.69380616
#> Ugt8a   -0.3790739  1.93586406 -0.04246824
#> Arpp19   0.5250832 -0.07853379  0.23483831
#> Lamp5    0.3373262  0.33003953 -0.78180268
#> Galnt6   1.1568725 -0.37853437  2.02219747
#> Hlf      0.7236919  0.07204898  0.06399838
#> Hs3st2   1.7543239  2.79683496  0.62673856
#> Tbr1     0.4543554 -0.12795061  0.52247349
#> Myl4    -1.2208226 -1.63717633  0.49065762
#> Cygb     0.6999679 -0.18816551 -1.15834089
#> Ttc9b   -1.1161517  1.68410097  1.98572787
#> Ipcef1  -2.3472564 -1.67428133 -0.51518959