This function converts a list of marker genes for different cell types or clusters into a matrix, where rows represent cell types and columns represent marker genes. The matrix contains the frequency of each marker gene across the different cell types.
markerList2mat(markerList)A list where each element contains marker genes for different cell types or clusters. Each element of the list is a named list, where the names are the cell types and the values are the marker genes for that cell type. Generally, it is a list of the output of function marker.select.
A matrix with rows representing cell types and columns representing unique marker genes. The values in the matrix represent the frequency of each gene as a marker in the corresponding cell type.
marker.select for select markers.
find.sig.genes for signature gene list.
data(toydata)
markers <- toydata$markers
marker.freq <- markerList2mat(list(markers))
print(marker.freq)
#> CCDC80 CRISPLD2 DPT FBLN1 LUM MMP2 PDGFRA PTGDS AGR3 ESR1
#> CAFs 1 1 1 1 1 1 1 1 0 0
#> Cancer Epithelial 0 0 0 0 0 0 0 0 1 1
#> Endothelial 0 0 0 0 0 0 0 0 0 0
#> Myeloid 0 0 0 0 0 0 0 0 0 0
#> Normal Epithelial 0 0 0 0 0 0 0 0 0 0
#> Plasmablasts 0 0 0 0 0 0 0 0 0 0
#> PVL 0 0 0 0 0 0 0 0 0 0
#> T-cells 0 0 0 0 0 0 0 0 0 0
#> FASN FOXA1 LYPD3 MLPH RHOH SCD BTNL9 EGFL7 HOXD9 IL3RA KDR
#> CAFs 0 0 0 0 0 0 0 0 0 0 0
#> Cancer Epithelial 1 1 1 1 1 1 0 0 0 0 0
#> Endothelial 0 0 0 0 0 0 1 1 1 1 1
#> Myeloid 0 0 0 0 0 0 0 0 0 0 0
#> Normal Epithelial 0 0 0 0 0 0 0 0 0 0 0
#> Plasmablasts 0 0 0 0 0 0 0 0 0 0 0
#> PVL 0 0 0 0 0 0 0 0 0 0 0
#> T-cells 0 0 0 0 0 0 0 0 0 0 0
#> SOX17 SOX18 VWF AIF1 C1QC CD86 FCER1G HAVCR2 IGSF6 ITGAX MNDA
#> CAFs 0 0 0 0 0 0 0 0 0 0 0
#> Cancer Epithelial 0 0 0 0 0 0 0 0 0 0 0
#> Endothelial 1 1 1 0 0 0 0 0 0 0 0
#> Myeloid 0 0 0 1 1 1 1 1 1 1 1
#> Normal Epithelial 0 0 0 0 0 0 0 0 0 0 0
#> Plasmablasts 0 0 0 0 0 0 0 0 0 0 0
#> PVL 0 0 0 0 0 0 0 0 0 0 0
#> T-cells 0 0 0 0 0 0 0 0 0 0 0
#> C5orf46 KRT14 KRT15 KRT16 KRT5 KRT6B MYH11 PIGR CD27 CD79A
#> CAFs 0 0 0 0 0 0 0 0 0 0
#> Cancer Epithelial 0 0 0 0 0 0 0 0 0 0
#> Endothelial 0 0 0 0 0 0 0 0 0 0
#> Myeloid 0 0 0 0 0 0 0 0 0 0
#> Normal Epithelial 1 1 1 1 1 1 1 1 0 0
#> Plasmablasts 0 0 0 0 0 0 0 0 1 1
#> PVL 0 0 0 0 0 0 0 0 0 0
#> T-cells 0 0 0 0 0 0 0 0 0 0
#> DERL3 ITM2C MZB1 PRDM1 SLAMF7 TNFRSF17 ANGPT2 AQP1 AVPR1A
#> CAFs 0 0 0 0 0 0 0 0 0
#> Cancer Epithelial 0 0 0 0 0 0 0 0 0
#> Endothelial 0 0 0 0 0 0 0 0 0
#> Myeloid 0 0 0 0 0 0 0 0 0
#> Normal Epithelial 0 0 0 0 0 0 0 0 0
#> Plasmablasts 1 1 1 1 1 1 0 0 0
#> PVL 0 0 0 0 0 0 1 1 1
#> T-cells 0 0 0 0 0 0 0 0 0
#> CAV1 EGFR PDGFRB TCEAL7 ZEB1 CCL5 CD247 CD3D CD3E CD3G CD69
#> CAFs 0 0 0 0 0 0 0 0 0 0 0
#> Cancer Epithelial 0 0 0 0 0 0 0 0 0 0 0
#> Endothelial 0 0 0 0 0 0 0 0 0 0 0
#> Myeloid 0 0 0 0 0 0 0 0 0 0 0
#> Normal Epithelial 0 0 0 0 0 0 0 0 0 0 0
#> Plasmablasts 0 0 0 0 0 0 0 0 0 0 0
#> PVL 1 1 1 1 1 0 0 0 0 0 0
#> T-cells 0 0 0 0 0 1 1 1 1 1 1
#> GZMA KLRB1
#> CAFs 0 0
#> Cancer Epithelial 0 0
#> Endothelial 0 0
#> Myeloid 0 0
#> Normal Epithelial 0 0
#> Plasmablasts 0 0
#> PVL 0 0
#> T-cells 1 1