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mahlon
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@mahlon-19973
Last seen 5.2 years ago
The function toTable() is supposed to create a data frame summarizing the output of a filter operation. This would be a nice way to get the number of cells in a multiple filter result, however, the function doesn't work for me. Minimal reproducible example is running the code contained in the documentation for the function:
## Loading example data, creating and applying a curv1Filter
dat <- read.FCS(system.file("extdata","0877408774.B08",
package="flowCore"))
c1f <- curv1Filter(filterId="myCurv1Filter", x=list("FSC-H"), bwFac=2)
fres <- filter(dat, c1f)
## creating and showing the summary
summary(fres)
s <- summary(fres)
## subsetting
s[[1]]
s[["peak 2"]]
##accessing details
s$true
s$n
toTable(s)
Traceback:
rest: 3581 of 10000 events (35.81%)
peak 1: 331 of 10000 events (3.31%)
peak 2: 5575 of 10000 events (55.75%)
peak 3: 455 of 10000 events (4.55%)
peak 4: 58 of 10000 events (0.58%)
> > > Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘toTable’ for signature ‘"filterSummary"’
> traceback()
3: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
2: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character,
""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list("filterSummary"), new("standardGeneric", .Data = function (x)
standardGeneric("toTable"), generic = "toTable", package = "AnnotationDbi",
group = list(), valueClass = character(0), signature = "x",
default = NULL, skeleton = (function (x)
stop("invalid call in method dispatch to 'toTable' (no default method)",
domain = NA))(x)), <environment>)
1: toTable(s)
Session Info:
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.32.1 ggcyto_1.10.2 ggplot2_3.1.0 geneplotter_1.60.0 annotate_1.60.0 XML_3.98-1.16 AnnotationDbi_1.44.0
[8] IRanges_2.16.0 S4Vectors_0.20.1 Biobase_2.42.0 BiocGenerics_0.28.0 flowFP_1.40.1 flowStats_3.40.1 flowWorkspace_3.28.2
[15] ncdfFlow_2.28.1 BH_1.69.0-1 RcppArmadillo_0.9.200.7.0 cluster_2.0.7-1 fda_2.4.8 Matrix_1.2-15 flowUtils_1.46.1
[22] flowViz_1.46.1 lattice_0.20-38 flowCore_1.48.1 colorspace_1.4-0
loaded via a namespace (and not attached):
[1] bit64_0.9-7 assertthat_0.2.0 BiocManager_1.30.4 latticeExtra_0.6-28 blob_1.1.1 robustbase_0.93-3 pillar_1.3.1 RSQLite_2.1.1 glue_1.3.0
[10] RUnit_0.4.32 digest_0.6.18 RColorBrewer_1.1-2 plyr_1.8.4 pcaPP_1.9-73 pkgconfig_2.0.2 zlibbioc_1.28.0 xtable_1.8-3 purrr_0.3.0
[19] corpcor_1.6.9 mvtnorm_1.0-8 scales_1.0.0 tibble_2.0.1 withr_2.1.2 lazyeval_0.2.1 hexbin_1.27.2 magrittr_1.5 crayon_1.3.4
[28] IDPmisc_1.1.19 mclust_5.4.2 memoise_1.1.0 ks_1.11.4 MASS_7.3-51.1 graph_1.60.0 tools_3.5.0 data.table_1.12.0 matrixStats_0.54.0
[37] stringr_1.4.0 munsell_0.5.0 bindrcpp_0.2.2 compiler_3.5.0 rlang_0.3.1 RCurl_1.95-4.11 grid_3.5.0 bitops_1.0-6 gtable_0.2.0
[46] DBI_1.0.0 rrcov_1.4-7 R6_2.4.0 gridExtra_2.3 dplyr_0.8.0.1 bit_1.1-14 bindr_0.1.1 KernSmooth_2.23-15 Rgraphviz_2.26.0
[55] stringi_1.3.1 Rcpp_1.0.0 DEoptimR_1.0-8 tidyselect_0.2.5
Your reproducible example seems incomplete, as
curv.filterwas never defined. I assume by "code contained in the documentation for the function", you mean effectively this:But I can't reproduce your dispatch error from that, as the last line produces the expected output:
I'll keep trying to find the cause of your error, but if you could update the reproducible example to the precise code that brought about the error it will help me out. Thanks.
Updated and, yes, the code you used is what I also used. I get the same error w/ other gate types and datasets too, FWIW.
Thank you for the response and any additional assistance you can provide.