Hi!

I am trying to filter a MAF by removing its variants by coordinates. To do that, I have a dataframe with 3 columns (chr, start, end). My problem is that I can only use subsetMaf to do that, as filterMaf has no "ranges" option. By subsetting, I can only get those variants occuring in the regions of the data frame, while I am looking for the variants NOT occuring there.

I have tryed to subset the MAF in order to get those variants that I want to remove, and then I have used setdiffMaf to get those variants which are different between this set and the original one, but I am getting the following error.

maf2 <- subsetMaf(maf, ranges = mydf)
expectedmaf <- setdiffMAF(maf1, maf2, refAltMatch = F)

Error in :=(maf_slot, NULL) : Check that is.data.table(DT) == TRUE. Otherwise, := and :=(...) are defined for use in j, once only and in particular ways. See help(":=").

sessionInfo( )

R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                  
[5] LC_TIME=Spanish_Spain.1252    

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

other attached packages:
[1] data.table_1.14.0 bedr_1.0.7        dplyr_1.0.4       ggplot2_3.3.5     maftools_2.6.05   xlsx_0.6.5       

loaded via a namespace (and not attached):
 [1] formatR_1.11         pillar_1.6.4         compiler_4.0.4       RColorBrewer_1.1-2   BiocManager_1.30.16  futile.logger_1.4.3  R.methodsS3_1.8.1   
 [8] R.utils_2.11.0       futile.options_1.0.1 tools_4.0.4          pkgload_1.2.3        testthat_3.0.2       lifecycle_1.0.1      tibble_3.0.6        
[15] gtable_0.3.0         lattice_0.20-41      pkgconfig_2.0.3      rlang_0.4.10         Matrix_1.3-2         DBI_1.1.1            parallel_4.0.4      
[22] yaml_2.2.1           VennDiagram_1.6.20   rJava_0.9-13         withr_2.4.2          desc_1.4.0           generics_0.1.1       xlsxjars_0.6.1      
[29] vctrs_0.3.8          rprojroot_2.0.2      grid_4.0.4           tidyselect_1.1.1     glue_1.4.2           R6_2.5.1             fansi_0.4.2         
[36] survival_3.2-7       lambda.r_1.2.4       purrr_0.3.4          magrittr_2.0.1       scales_1.1.1         ellipsis_0.3.2       splines_4.0.4       
[43] assertthat_0.2.1     colorspace_2.0-0     utf8_1.1.4           munsell_0.5.0        crayon_1.4.1         R.oo_1.24.0

Do you know how can I solve this? or if there is an easiest way to filter a maf by coordinates?

Hello,

So, I've had the same problem and tried running the function line by line with two MAFs. When the function is running it's adding a 'maf_slot' column where the values can be 'syn' or 'nonsyn'. I've noticed that all the values I have are 'nonsyn'. I removed the parts where the function uses maf_x_unique[['syn']] like below and it works. So basically, if you have all synonymous or all non-synonymous variants the default function doesn't work.

if (!mafObj) {
maf_x_unique


} else {
maf_x_unique = split(maf_x_unique, f = maf_x_unique$maf_slot)
#maf_x_unique[['syn']][,maf_slot := NULL]
maf_x_unique[['nonsyn']][,maf_slot := NULL]


#maf_x_unique = MAF(nonSyn = maf_x_unique[['nonsyn']], syn = maf_x_unique[['syn']], clinicalData = x@clinical.data, verbose = FALSE)
maf_x_unique = MAF(nonSyn = maf_x_unique[['nonsyn']], clinicalData = x@clinical.data, verbose = FALSE)
maf_x_unique@clinical.data = droplevels(maf_x_unique@clinical.data)

#mafSummary = summarizeMaf(maf = maf_x_unique[["nonsyn"]], anno = x@clinical.data, chatty = FALSE)
# maf_x_unique = MAF(data = maf_x_unique[['nonsyn']], variants.per.sample = mafSummary$variants.per.sample, variant.type.summary = mafSummary$variant.type.summary,
#         variant.classification.summary = mafSummary$variant.classification.summary, gene.summary = mafSummary$gene.summary,
#         summary = mafSummary$summary, maf.silent = maf_x_unique[['syn']], clinical.data = droplevels(mafSummary$sample.anno))
  }