Closed ghost closed 2 years ago
cytoset
should work
> cs <- load_cytoset_from_fcs(files = file_list, emptyValue = FALSE, alter.names = TRUE)
> gs <- GatingSet(cs)
The reason you see these empty s4 slots contents is because these are inherited from flowSet
s4 class and not actually used by cytoset
. So the real data structures are hidden behind the external pointer (in c++), i.e.
> cs@pointer
<pointer: 0x56356e303f60>
and can be accessed by the cytoset
accessors (i.e. s4 methods)
> cs
A cytoset with 2 samples.
column names:
FSC-HLin, SSC-HLin, GRN-HLog, YEL-HLog, RED-HLog, NIR-HLog, RED2-HLog, NIR2-HLog, FSC-HLog, SSC-HLog, GRN-HLin, YEL-HLin, RED-HLin, NIR-HLin, RED2-HLin, NIR2-HLin, NIR2-A, NIR2-ALog, NIR2-W
> cs[[1]]
cytoframe object 'C2210_CD5_CD45_CD14.fcs'
with 9310 cells and 19 observables:
name desc range minRange maxRange
$P1 FSC-HLin Forward Scatter (FSC.. 1023 0.00000 1023
$P2 SSC-HLin Side Scatter (SSC-HL.. 1023 0.00000 1023
$P3 GRN-HLog Green Fluorescence (.. 10000 1.00904 10000
$P4 YEL-HLog Yellow Fluorescence .. 10000 1.00904 10000
$P5 RED-HLog Red Fluorescence (RE.. 10000 1.00904 10000
... ... ... ... ... ...
$P15 RED2-HLin Red2 Fluorescence (R.. 1023 0 1023
$P16 NIR2-HLin Near IR2 (NIR2-HLin) 1023 0 1023
$P17 NIR2-A Near IR2 Area (NIR2-A) 1023 0 1023
$P18 NIR2-ALog Near IR2 Area (NIR2-.. 1023 0 1023
$P19 NIR2-W Near IR2 Width (NIR2.. 1023 0 1023
318 keywords are stored in the 'description' slot
row names(0):
I know it maybe confusing but s4 slots are not supposed to be accessed directly by user anyway.
Thank you so much! (I am clearly a newbie!) I was indeed confused.
Hi Mike, Greg and the team, I am having a very similar issue as issue 341 but the solution of install newer version of cytolib and flowWorkspace and flowCore doesn't seem to fix the issue.
I can create flowset without problem using read.flowset() but the GatingSet is returning an error. `
in addition, (this might be related?), if I start from a cytoset with load_cytoset_from_fcs() return an empty cytoSet... using:
cs <- load_cytoset_from_fcs(files = file_list, emptyValue = FALSE, alter.names = TRUE)
The FCS files that I am trying to analyze were created with a guava (FCS version 2.0). Here is an example of the file (2x) I used: Archive.zip Here is the session info():
`> sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.5.2
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats graphics grDevices utils datasets methods base
other attached packages: [1] flowWorkspace_4.5.3 flowCore_2.5.0 cytolib_2.5.3
loaded via a namespace (and not attached): [1] Rcpp_1.0.7 RColorBrewer_1.1-2 compiler_4.1.0 pillar_1.6.2
[5] base64enc_0.1-3 tools_4.1.0 zlibbioc_1.38.0 aws.s3_0.3.21
[9] digest_0.6.27 lattice_0.20-44 lifecycle_1.0.0 tibble_3.1.4
[13] png_0.1-7 pkgconfig_2.0.3 rlang_0.4.11 graph_1.70.0
[17] DBI_1.1.1 Rgraphviz_2.36.0 curl_4.3.2 parallel_4.1.0
[21] httr_1.4.2 dplyr_1.0.7 xml2_1.3.2 generics_0.1.0
[25] S4Vectors_0.30.0 vctrs_0.3.8 stats4_4.1.0 grid_4.1.0
[29] tidyselect_1.1.1 glue_1.4.2 data.table_1.14.0 Biobase_2.52.0
[33] R6_2.5.1 jpeg_0.1-9 fansi_0.5.0 XML_3.99-0.7
[37] latticeExtra_0.6-29 purrr_0.3.4 RProtoBufLib_2.4.0 magrittr_2.0.1
[41] scales_1.1.1 matrixStats_0.60.1 ellipsis_0.3.2 BiocGenerics_0.38.0 [45] assertthat_0.2.1 colorspace_2.0-2 aws.signature_0.6.0 ncdfFlow_2.38.0
[49] utf8_1.2.2 munsell_0.5.0 RcppParallel_5.1.4 crayon_1.4.1 `
Hope this help! Let me know if you need more information or if I missed anything in the previous issues.
Best, Stephane