Cell type signatures
cell_signatures.RdCell type signatures
Examples
## to use cell signatures, type
data(cell_signatures)
data(vaccination)
gl <- vaccination$GeneName[ order(vaccination$qval.F.D1) ]
tmodCERNOtest(gl, mset=cell_signatures)
#> ID Title cerno N1 AUC
#> CM00043 CM00043 Sertoli cell 149.64473 41 0.6674980
#> CM00030 CM00030 Myoepithelial cell 260.10985 85 0.5930265
#> CM00021 CM00021 Hepatocyte 51.72331 9 0.8268388
#> PG00057 PG00057 Glutaminergic neurons 44.00250 7 0.8343856
#> PG00094 PG00094 Neural stem/precursor cell 70.24000 16 0.6995704
#> PG00051 PG00051 GABAergic neurons 38.31131 6 0.8161530
#> CS00066 CS00066 T cells regulatory (Tregs) top50 50.14813 10 0.7229767
#> CS00065 CS00065 T cells regulatory (Tregs) top25 67.42724 16 0.7052620
#> PG00056 PG00056 Glomus cell 28.43640 4 0.9538843
#> PG00019 PG00019 Cholangiocytes 24.49107 3 0.9177785
#> PG00020 PG00020 Chondrocytes 24.49107 3 0.9177785
#> PG00151 PG00151 Undefined placental cell 44.89206 9 0.7539329
#> CS00039 CS00039 NK cells activated top50 31.24662 5 0.8755221
#> PG00054 PG00054 Gastric chief cell 40.72987 8 0.6681803
#> PG00039 PG00039 Enterocytes 29.93360 5 0.8378637
#> PG00042 PG00042 Ependymal cell 29.93360 5 0.8378637
#> PG00055 PG00055 Germ cell 18.52657 2 0.9907661
#> CS00046 CS00046 T cells CD4 memory activated top10 24.96178 4 0.7750684
#> PG00053 PG00053 Gamma delta T cell 24.52972 4 0.7795175
#> PG00048 PG00048 Fibroblasts 37.15059 8 0.7227553
#> PG00007 PG00007 Anterior pituitary gland cell 12.37926 1 0.9982906
#> PG00059 PG00059 Granulosa cell 20.10104 3 0.8033983
#> CS00037 CS00037 NK cells activated top10 19.76089 3 0.8194777
#> cES P.Value adj.P.Val
#> CM00043 1.824936 7.484170e-06 0.001386660
#> CM00030 1.530058 1.046536e-05 0.001386660
#> CM00021 2.873517 4.125684e-05 0.003644355
#> PG00057 3.143035 5.914313e-05 0.003918232
#> PG00094 2.195000 1.103051e-04 0.005846168
#> PG00051 3.192609 1.365601e-04 0.006031406
#> CS00066 2.507406 2.109163e-04 0.007984687
#> CS00065 2.107101 2.505869e-04 0.008300693
#> PG00056 3.554550 3.980025e-04 0.009485925
#> PG00019 4.081844 4.240428e-04 0.009485925
#> PG00020 4.081844 4.240428e-04 0.009485925
#> PG00151 2.494003 4.295513e-04 0.009485925
#> CS00039 3.124662 5.341466e-04 0.010888373
#> PG00054 2.545617 6.085874e-04 0.011519690
#> PG00039 2.993360 8.783254e-04 0.014547264
#> PG00042 2.993360 8.783254e-04 0.014547264
#> PG00055 4.631641 9.734052e-04 0.015173670
#> CS00046 3.120222 1.577911e-03 0.023230361
#> PG00053 3.066215 1.866823e-03 0.025876379
#> PG00048 2.321912 1.997084e-03 0.025876379
#> PG00007 6.189632 2.050581e-03 0.025876379
#> PG00059 3.350174 2.656998e-03 0.032004747
#> CS00037 3.293481 3.054180e-03 0.035189460