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)

Arguments

sc
SingleCellAssay
na.rm
should NAs be removed, or carried through?

Value

vector of proportions

Functions

  • 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.

Examples

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