lollipopPlot2 and lollipopPlot parse protein variants differently

[lbeltrame]

Describe the issue As an example:

• R1443* in BRCA1 is correctly plotted by lollipopPlot
• R1443* is discarded by get_lp_data invoked by lollipopPlot2

This also happens with HGVSp notation, e.g. p.Arg1443Ter.

A cursory look at the code seems to indicate that the regexes which parse the protein change are different in the two functions: lollipopPlot does not use get_lp_data at all.

Session info

R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8

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

other attached packages:
[1] maftools_2.6.05

loaded via a namespace (and not attached):
 [1] lattice_0.20-41    ps_1.6.0           fansi_0.4.2        crayon_1.4.1       utf8_1.2.1         grid_4.0.5         R6_2.5.0           lifecycle_1.0.0
 [9] magrittr_2.0.1     pillar_1.6.0       cli_2.5.0          rlang_0.4.10       rstudioapi_0.13    data.table_1.14.0  Matrix_1.3-2       vctrs_0.3.7
[17] ellipsis_0.3.1     splines_4.0.5      RColorBrewer_1.1-2 tools_4.0.5        readr_1.4.0        glue_1.4.2         hms_1.0.0          survival_3.2-11
[25] compiler_4.0.5     pkgconfig_2.0.3    tibble_3.1.1

[lbeltrame]

The reason is in https://github.com/PoisonAlien/maftools/blob/a62aa15ee561363615bf17d8d1fff3c9a7833d1e/R/get_lp_data.R#L28

If there's another column called AAChange, it is not replaced, and therefore the code gets confused and picks the wrong one, causing parsing errors.

[PoisonAlien]

Hi,

Thanks for going through the code. Does it work as expected if you change your column name (in the MAF) to other than AAChange?

[lbeltrame]

Yes, it does.

[github-actions[bot]]

This issue is stale because it has been open for 60 days with no activity.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.