subset .data outside of a data mask context error

[shanshenbing]

Hello, thank you for your software!
When I run the following command:
results <- pipelineCNA(count_mtx = count_mtx)

I got this:

[1] "found 5 subclones"
percentage_cells_subsclone_1 percentage_cells_subsclone_2 percentage_cells_subsclone_3 percentage_cells_subsclone_4
0.26827012 0.23589269 0.32562442 0.13135985
percentage_cells_subsclone_5
0.03885291
[1] "Segmentation of subclone : 1"
[1] "Segmentation of subclone : 2"
[1] "Segmentation of subclone : 3"
[1] "Segmentation of subclone : 4"
[1] "Segmentation of subclone : 5"
$_subclone1
Chr Start End Alteration segm.mean
88 19 42086110 46788594 -1 -0.130204

$_subclone2
Chr Start End Alteration segm.mean
5 1 174159410 201171574 -2 -0.247542
81 16 53055033 57385048 2 0.367030
45 9 84668551 99970341 -1 -0.118025
60 12 190077 6942321 1 0.145254
94 19 42086110 54670359 -1 -0.127578

$_subclone3
Chr Start End Alteration segm.mean
5 1 168225938 193254815 -1 -0.118066
63 10 21756537 73625953 -1 -0.121260
66 10 126905409 133421307 1 0.156538
75 12 53507856 57132139 1 0.158576

$_subclone4
Chr Start End Alteration segm.mean
49 9 136440096 137870016 1 0.148681
56 12 6942978 13000273 -1 -0.176305
86 19 281040 2096673 1 0.156774
89 19 39391303 49878459 -1 -0.181592

$_subclone5
Chr Start End Alteration segm.mean
3 1 150265399 153986358 2 0.140948
2 1 51236271 150236156 -1 -0.084311
6 1 160995211 205532793 -1 -0.094113
14 3 149517235 197956610 -1 -0.118140
16 4 53377643 82044244 1 0.138069
23 5 134738501 140303121 -1 -0.147511
63 14 73275107 91510554 -1 -0.104558
85 19 16185380 23395560 1 0.148158

$_clone
Chr Start End Alteration segm.mean
76 17 31317560 38853843 -2 -0.404099

$_shareSubclone
Chr Start End Alteration segm.mean sh_sub Mean
_share1.1 2 99337353 120294713 -2 -0.221323 1-3-4 0
_share2.9 2 101696850 127388465 -2 -0.364826 2-3 0
_share1.3 6 30617709 32180793 -2 -0.096464 1-3-4 0
_share2.27 6 30617709 31959110 -2 -0.215626 2-5 0
_share3.3 6 30617709 31817946 -2 -0.158026 3-1-4 0
_share1.5 6 125781161 170407065 -1 -0.141146 1-2-3-4 0
_share2.1 6 127968779 170407065 -1 -0.140886 2-1-3-4 0
_share3.5 6 129576132 170407065 -1 -0.183996 3-1-2-4 0
_share1.46 10 50305586 70233911 -1 -0.124966 1-2 0
_share2.11 10 50305586 69401882 -1 -0.142419 2-1-5 0
_share1.11 11 167784 915058 1 0.187518 1-3-5 0
_share2.56 11 167784 1012245 2 0.213686 2-3 0
_share2.12 17 31317560 38853843 -2 -0.176035 2-1-3-4 0

Error:
! Can't subset .data outside of a data mask context.
can you help me with the error?

When running the command with the data you provided, I got the same error:

load('./MGH106_data.RData')
#myobj <- load(file = './listCountMtx.RData')
results <- SCEVAN::pipelineCNA(count_mtx, sample = "MGH106", par_cores = 20, SUBCLONES = TRUE, plotTree = TRUE)

$MGH106_shareSubclone
Chr Start End Alteration segm.mean sh_sub Mean
MGH106_share1.4 1 23964804 27336400 -2 -0.246198 1-2 0
MGH106_share3.4 1 25818640 28643085 -2 -0.211230 3-2 0
......
MGH106_share2.242 22 36189124 39532855 -2 -0.210030 2-1 0

Error:
! Can't subset .data outside of a data mask context.
Run rlang::last_error() to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)

[AntonioDeFalco]

It probably concerns your version of dplyr, which version do you have installed?

[shanshenbing]

Thank you for the quick answer. My dplyr version is 1.0.8. I'll try a newer version of dplyr and check the result.

[shanshenbing]

I updated my dplyr to 1.0.10 and run tutorial as this:
library(SCEVAN)
library(dplyr)
load('./MGH106_data.RData')
#myobj <- load(file = './listCountMtx.RData')

results <- SCEVAN::pipelineCNA(count_mtx, sample = "MGH106", par_cores = 20, SUBCLONES = TRUE, plotTree = TRUE)

unfortunately, I got same error.
ttaching package: ‘ggtree’

The following object is masked from ‘package:ape’:

rotate

The following object is masked from ‘package:IRanges’:

collapse

The following object is masked from ‘package:S4Vectors’:

expand

Error:
! Can't subset .data outside of a data mask context.
Run rlang::last_error() to see where the error occurred.

Here is my session info:

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] ggtree_2.4.2 ape_5.5 tidytree_0.3.4 ggplot2_3.3.6
[5] Rtsne_0.15 igraph_1.2.11 scran_1.18.7 SingleCellExperiment_1.12.0
[9] SummarizedExperiment_1.20.0 Biobase_2.50.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
[13] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.1 MatrixGenerics_1.2.1
[17] matrixStats_0.62.0 yaGST_2017.08.25 doParallel_1.0.16 iterators_1.0.13
[21] foreach_1.5.1 dplyr_1.0.10 SCEVAN_1.0.1

loaded via a namespace (and not attached):
[1] nlme_3.1-152 bitops_1.0-7 RColorBrewer_1.1-3 tools_4.0.5
[5] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
[9] lazyeval_0.2.2 colorspace_2.0-3 withr_2.4.2 tidyselect_1.1.1
[13] compiler_4.0.5 parallelDist_0.2.4 textshaping_0.3.6 cli_3.3.0
[17] BiocNeighbors_1.8.2 DelayedArray_0.16.3 labeling_0.4.2 scales_1.1.1
[21] systemfonts_1.0.2 digest_0.6.29 XVector_0.30.0 pkgconfig_2.0.3
[25] sparseMatrixStats_1.2.1 limma_3.46.0 rlang_1.0.4 rstudioapi_0.13
[29] DelayedMatrixStats_1.12.3 farver_2.1.0 generics_0.1.0 jsonlite_1.7.2
[33] BiocParallel_1.24.1 RCurl_1.98-1.5 magrittr_2.0.1 BiocSingular_1.6.0
[37] GenomeInfoDbData_1.2.4 scuttle_1.0.4 patchwork_1.1.1 Matrix_1.3-3
[41] Rcpp_1.0.6 munsell_0.5.0 fansi_0.4.2 lifecycle_1.0.1
[45] yaml_2.2.1 edgeR_3.32.1 zlibbioc_1.36.0 grid_4.0.5
[49] dqrng_0.3.0 crayon_1.5.1 lattice_0.20-44 beachmat_2.6.4
[53] locfit_1.5-9.4 pillar_1.8.0 codetools_0.2-18 glue_1.6.0
[57] BiocManager_1.30.16 RcppParallel_5.1.4 treeio_1.14.4 vctrs_0.4.1
[61] gtable_0.3.0 purrr_0.3.4 tidyr_1.2.0 assertthat_0.2.1
[65] rsvd_1.0.5 ragg_1.1.3 tibble_3.1.8 pheatmap_1.0.12
[69] aplot_0.0.6 rvcheck_0.1.8 bluster_1.0.0 statmod_1.4.36

Hope for help.

[AntonioDeFalco]

Hi @shanshenbing.
I found the problem that unfortunately depends on ggtree library which I use to make the Phylogenetic tree graph that necessarily wants version 1.05 of dplyr otherwise it gives this error (YuLab-SMU/ggtree#399).

While I find the solution to this error, you can either disable this graph with the parameter plotTree=FALSE or install the old 1.05 version of dplyr.

Thanks. Regards

[shanshenbing]

Thank you for your hard work. I get it!