Hi Everyone! I have a question regarding the FlowCore summary usage applied to the result of a filter. Here´s the thing. I am analysing Flow Cytometry data. I first gated for single cells using two types of automatic gates from OpenCyto (Boundarygate and SingletGate). Then I wanted to define the population of positive cells for a fluorophore in this way: take the neagtive control, without fluorophore, and define the gate that includes the 1% of cells with highest fluorescence. Then I apply this gate to all my other populations(frames). The gating per se works but I have problems in obtaining a summary of the results of the filtering process. Unfortunately this is quite an important information that I need to know. the weird thing is that the other gates that I applied, with similar coding, produced a nice summary with the percentage of cells within the gate. How come that with this specific filter it doesn´t work? And what could I do to solve the problem? I specify that I only started to use R quite recently.
chnl <- "DsRed.dt.Tomato...583.22...A" xistpos <- openCyto:::.quantileGate(TSingletsMyFlowSet[[29]], channels = chnl, probs = 0.99) p <- autoplot(TSingletsMyFlowSet[[29]], chnl) p + geomgate(xistpos) filter(TSingletsMyFlowSet[[29]], xistpos) A filterResult produced by the filter named '' #<-**It doesn´t recognize that the name of the gate is xistpos result3 = filter(TSingletsMyFlowSet[[29]], xistpos) #there's a bug that does not return me the result statistics result3 A filterResult produced by the filter named '' summary(result3) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘identifier<-’ for signature ‘"NULL", "character"’
sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LCCOLLATE=EnglishUnited Kingdom.1252
[2] LCCTYPE=EnglishUnited Kingdom.1252
[3] LCMONETARY=EnglishUnited Kingdom.1252
[4] LCNUMERIC=C
[5] LCTIME=English_United Kingdom.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] openCyto1.24.0 ggcyto1.14.1
[3] ncdfFlow2.32.0 BH1.72.0-3
[5] RcppArmadillo0.9.850.1.0 ggplot23.3.0
[7] flowCore1.52.1 flowWorkspace3.34.1
[9] flowStats3.44.0 flowAI1.16.0
loaded via a namespace (and not attached):
[1] Biobase2.46.0 splines3.6.1 R.utils2.9.2
[4] ellipse0.4.1 gtools3.8.1 RcppParallel5.0.0
[7] assertthat0.2.1 BiocManager1.30.10 stats43.6.1
[10] latticeExtra0.6-29 RBGL1.62.1 robustbase0.93-6
[13] pillar1.4.3 lattice0.20-40 glue1.3.2
[16] digest0.6.25 RColorBrewer1.1-2 colorspace1.4-1
[19] htmltools0.4.0 Matrix1.2-18 R.oo1.23.0
[22] plyr1.8.6 pcaPP1.9-73 pkgconfig2.0.3
[25] fda2.4.8.1 zlibbioc1.32.0 purrr0.3.3
[28] corpcor1.6.9 mvtnorm1.1-0 scales1.1.0
[31] jpeg0.1-8.1 tibble2.1.3 farver2.0.3
[34] withr2.1.2 flowViz1.50.0 BiocGenerics0.32.0
[37] hexbin1.28.1 mnormt1.5-6 magrittr1.5
[40] crayon1.3.4 IDPmisc1.1.20 mclust5.4.5
[43] evaluate0.14 ks1.11.7 R.methodsS31.8.0
[46] MASS7.3-51.5 changepoint2.2.2 graph1.64.0
[49] tools3.6.1 data.table1.12.8 flowClust3.24.0
[52] lifecycle0.2.0 matrixStats0.56.0 stringr1.4.0
[55] munsell0.5.0 cluster2.1.0 compiler3.6.1
[58] rlang0.4.5 grid3.6.1 rstudioapi0.11
[61] labeling0.3 rmarkdown2.1 gtable0.3.0
[64] reshape21.4.3 rrcov1.5-2 R62.4.1
[67] zoo1.8-7 gridExtra2.3 knitr1.28
[70] dplyr0.8.5 clue0.3-57 KernSmooth2.23-16
[73] Rgraphviz2.30.0 stringi1.4.6 parallel3.6.1
[76] Rcpp1.0.3 png0.1-7 DEoptimR1.0-8
[79] tidyselect1.0.0 xfun0.12
Best, Gemma
