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neilruthen
•
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@neilruthen-16682
Last seen 5.7 years ago
Hello,
While creating flow frames using the flowFrame function I noticed that while I could change the parameters of an existing flow frame using
"parameters(flowFrame)<-" , I could not use the function parameters(flowFrame) to extract the AnnotatedDataFrame.
When I attempt to use the flowCore parameters() function, the only function available is the parameters() function from the package
'modeltools'. Below is some code from my most recent R session:
> frames <- lapply(dir(path = "/Users/nruthen16/Desktop/MRD-/134", full.names=TRUE), read.FCS)
> frames[[1]]
flowFrame object 'd339ff7a-04fc-4f44-a74f-862590f6e7af'
with 500000 cells and 15 observables:
name desc range minRange maxRange
$P1 FSC-A <NA> 262144 0 262143
$P2 FSC-H <NA> 262144 0 262143
$P3 SSC-A <NA> 262144 1 10000
$P4 SSC-H <NA> 262144 1 10000
$P5 FITC-A CD15 262144 1 10000
$P6 PE-A CD33 262144 1 10000
$P7 PerCP-Cy5-5-A CD117 PC5 262144 1 10000
$P8 PE-Cy7-A CD13 262144 1 10000
$P9 APC-A CD34 262144 1 10000
$P10 Alexa Fluor 700-A CD71 262144 1 10000
$P11 APC-ALEXA750-A CD38 262144 1 10000
$P12 Pacific Blue-A HLADR 262144 1 10000
$P13 V500-A CD45 262144 1 10000
$P14 BV605-A CD19 262144 1 10000
$P15 Time <NA> 262144 0 262143
232 keywords are stored in the 'description' slot
> parameters(frames[[1]])
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘parameters’ for signature ‘"flowFrame"’
> 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("flowFrame"), new("standardGeneric", .Data = function (object,
...)
standardGeneric("parameters"), generic = "parameters", package = "modeltools",
group = list(), valueClass = character(0), signature = "object",
default = NULL, skeleton = (function (object, ...)
stop("invalid call in method dispatch to 'parameters' (no default method)",
domain = NA))(object, ...)), <environment>)
1: parameters(frames[[1]])
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.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 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.30.0 ranger_0.10.1 obliqueRF_0.3 mda_0.4-10 class_7.3-14 pls_2.6-0
[7] ROCR_1.0-7 gplots_3.0.1 party_1.3-0 strucchange_1.5-1 sandwich_2.4-0 zoo_1.8-3
[13] modeltools_0.2-22 mvtnorm_1.0-8 e1071_1.6-8 caret_6.0-80 lattice_0.20-35 berryFunctions_1.17.0
[19] circlize_0.4.4 ComplexHeatmap_1.18.1 randomForest_4.6-14 RColorBrewer_1.1-2 reshape2_1.4.3 FlowSOM_1.12.0
[25] igraph_1.2.1 ggcyto_1.8.2 flowWorkspace_3.28.1 ncdfFlow_2.26.0 BH_1.66.0-1 RcppArmadillo_0.8.600.0.0
[31] flowCore_1.46.1 ggplot2_3.0.0 reader_1.0.6 NCmisc_1.1.5
loaded via a namespace (and not attached):
[1] TH.data_1.0-9 colorspace_1.3-2 rjson_0.2.20 corpcor_1.6.9 GlobalOptions_0.1.0
[6] DRR_0.0.3 hexbin_1.27.2 IDPmisc_1.1.17 prodlim_2018.04.18 lubridate_1.7.4
[11] coin_1.2-2 codetools_0.2-15 splines_3.5.0 robustbase_0.93-1.1 knitr_1.20
[16] RcppRoll_0.3.0 broom_0.5.0 ddalpha_1.3.4 cluster_2.0.7-1 kernlab_0.9-26
[21] sfsmisc_1.1-2 graph_1.58.0 rrcov_1.4-4 compiler_3.5.0 proftools_0.99-2
[26] backports_1.1.2 assertthat_0.2.0 Matrix_1.2-14 lazyeval_0.2.1 tools_3.5.0
[31] bindrcpp_0.2.2 gtable_0.2.0 glue_1.3.0 dplyr_0.7.6 Rcpp_0.12.18
[36] Biobase_2.40.0 gdata_2.18.0 nlme_3.1-137 iterators_1.0.10 timeDate_3043.102
[41] gower_0.1.2 stringr_1.3.1 gtools_3.8.1 XML_3.98-1.12 DEoptimR_1.0-8
[46] zlibbioc_1.26.0 MASS_7.3-49 scales_0.5.0 ipred_0.9-6 parallel_3.5.0
[51] yaml_2.2.0 gridExtra_2.3 rpart_4.1-13 latticeExtra_0.6-28 stringi_1.2.4
[56] pcaPP_1.9-73 foreach_1.4.4 caTools_1.17.1.1 BiocGenerics_0.26.0 lava_1.6.2
[61] geometry_0.3-6 shape_1.4.4 flowViz_1.44.0 bitops_1.0-6 rlang_0.2.1
[66] pkgconfig_2.0.1 matrixStats_0.54.0 purrr_0.2.5 bindr_0.1.1 recipes_0.1.3
[71] CVST_0.2-2 tidyselect_0.2.4 plyr_1.8.4 magrittr_1.5 R6_2.2.2
[76] multcomp_1.4-8 dimRed_0.1.0 pillar_1.3.0 withr_2.1.2 survival_2.41-3
[81] abind_1.4-5 nnet_7.3-12 tibble_1.4.2 tsne_0.1-3 crayon_1.3.4
[86] KernSmooth_2.23-15 GetoptLong_0.1.7 data.table_1.11.4 Rgraphviz_2.24.0 ConsensusClusterPlus_1.44.0
[91] ModelMetrics_1.1.0 tidyr_0.8.1 munsell_0.5.0 magic_1.5-8
Any help on how to resolve this issue would be greatly appreciated!
Thanks,
Neil
