freq returns the frequency of expression, i.e., the proportion of non-zero values in sc.
NAs can be optionally removed
freq(sc, na.rm = TRUE)
condmean(sc)
condSd(sc)
numexp(sc)SingleCellAssay
should NAs be removed, or carried through?
vector of proportions
condmean: Report the mean non-zero expression value for each gene. NAs are always removed.
condSd: Report standard deviation of expression, for positive et for each gene. NAs are always removed.
numexp: Report number of expressing cells ($>0$) per gene. NAs are removed.
data(vbetaFA)
freq(vbetaFA)
#> B3GAT1 BAX BCL2 CCL2 CCL3 CCL4
#> 0.037280702 0.383771930 0.120614035 0.050438596 0.111842105 0.065789474
#> CCL5 CCR2 CCR4 CCR5 CCR7 CD109
#> 0.225877193 0.107456140 0.451754386 0.135964912 0.611842105 0.105263158
#> CD27 CD28 CD38 CD3d CD3g CD4
#> 0.355263158 0.600877193 0.114035088 0.701754386 0.429824561 0.453947368
#> CD40LG CD45 CD48 CD5 CD69 CD8a
#> 0.497807018 0.578947368 0.688596491 0.429824561 0.822368421 0.041666667
#> CSF1 CSF2 CTLA4 CTSD CXCL13 CXCR4
#> 0.149122807 0.059210526 0.173245614 0.337719298 0.008771930 0.655701754
#> DPP4 ENTPD1 EOMES FAS FASLG FOXP3
#> 0.375000000 0.072368421 0.096491228 0.355263158 0.144736842 0.171052632
#> GAPDH GATA3 GZMA HLADRA ICOS IFNg
#> 0.857456140 0.291666667 0.089912281 0.131578947 0.467105263 0.133771930
#> IL10 IL12RbII IL13 IL16 IL2 IL22
#> 0.155701754 0.048245614 0.032894737 0.567982456 0.166666667 0.048245614
#> IL2Ra IL2Rg IL3 IL4 IL6R IL6ST
#> 0.274122807 0.842105263 0.019736842 0.024122807 0.324561404 0.583333333
#> IL7R IL8 LIF MKI67 MMP9 NT5E
#> 0.734649123 0.133771930 0.087719298 0.006578947 0.054824561 0.083333333
#> PCNA PECAM1 PRDM1 PRF1 RORC SLAMF1
#> 0.074561404 0.160087719 0.414473684 0.114035088 0.078947368 0.129385965
#> SLAMF5 SLAMF7 TBX21 TGFB1 TIA1 TIMP1
#> 0.182017544 0.081140351 0.107456140 0.791666667 0.333333333 0.197368421
#> TNF TNFRSF9 TNFSF10
#> 0.280701754 0.133771930 0.357456140
condmean(vbetaFA)
#> B3GAT1 BAX BCL2 CCL2 CCL3 CCL4 CCL5 CCR2
#> 18.07574 18.65490 18.85990 20.53079 22.00138 21.46809 21.31843 19.48177
#> CCR4 CCR5 CCR7 CD109 CD27 CD28 CD38 CD3d
#> 18.80196 17.87613 19.22938 17.79209 16.70189 16.70333 18.28595 17.40692
#> CD3g CD4 CD40LG CD45 CD48 CD5 CD69 CD8a
#> 18.94420 14.30945 20.20845 17.81685 17.99315 18.34726 21.18820 18.40681
#> CSF1 CSF2 CTLA4 CTSD CXCL13 CXCR4 DPP4 ENTPD1
#> 18.94010 22.17711 18.20700 19.13220 13.74116 17.02459 19.05627 18.77306
#> EOMES FAS FASLG FOXP3 GAPDH GATA3 GZMA HLADRA
#> 17.97955 18.55322 19.13463 20.54223 21.73553 20.24077 18.64631 21.14664
#> ICOS IFNg IL10 IL12RbII IL13 IL16 IL2 IL22
#> 15.94952 21.16613 19.32013 17.10083 20.39037 16.92839 20.47439 20.33221
#> IL2Ra IL2Rg IL3 IL4 IL6R IL6ST IL7R IL8
#> 20.86631 20.66392 22.74347 20.29877 18.21137 17.79195 19.75589 19.90062
#> LIF MKI67 MMP9 NT5E PCNA PECAM1 PRDM1 PRF1
#> 19.11974 16.59201 21.17655 18.94020 18.51814 18.80501 19.32161 17.45388
#> RORC SLAMF1 SLAMF5 SLAMF7 TBX21 TGFB1 TIA1 TIMP1
#> 20.12078 15.53120 16.75542 16.63989 14.19542 20.64438 17.30637 18.90039
#> TNF TNFRSF9 TNFSF10
#> 18.06859 20.08218 17.47417