TMB plot (tcgaCompare): Burden changes depending on input order

[FriederikeHanssen]

Describe the issue I am using the funciton tcgaCompare. Depending on the whether I plot each of my cohorts individually or add them all to one tcgaCompare plot, the results change.

Command Please post your commands and the output (errors or any unexpected output)

Plot A (both):

tumor_mutational_burden <- tcgaCompare(
                               maf = c( mafs_wes,mafs_overlap),
                               capture_size = c(capture_size_wes,capture_size_overlap),
                               cohortName = c( "WES","Overlap )
                                )
tumor_mutational_burden

Plot B (one only):

tumor_mutational_burden <- tcgaCompare(mafs_wes, capture_size = capture_size_wes )
tumor_mutational_burden

Session info Run sessionInfo() and post the output below

karyoploteR       regioneR  GenomicRanges   GenomeInfoDb        IRanges      S4Vectors   BiocGenerics 
      "1.28.0"       "1.34.0"       "1.54.1"       "1.38.1"       "2.36.0"       "0.40.2"       "0.48.1" 
        ggpubr        ggplot2      gridExtra          tidyr          dplyr ComplexHeatmap     kableExtra 
       "0.6.0"        "3.5.1"          "2.3"        "1.3.1"        "1.1.4"       "2.18.0"        "1.3.4" 
         knitr        cowplot        forcats      patchwork       maftools 
        "1.45"        "1.1.3"        "1.0.0"        "1.1.3"       "2.18.0" 

[PoisonAlien]

Hi, Thank you for the issue. It was indeed a bug - all the input MAFs were being normalized with the first capture_size. I have fixed it. Please let me know if it works for you.

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