Shixiang Wang (王诗翔)
Shixiang Wang (王诗翔)
@brewert2 A minimal example dataset (along with code) can help develper check and debug this issue.
This typically means the input MAF data does not contain mutations that may have effects (on gene function). If you want to include all mutations, you should reset the `vc_nonSyn`...
@zyffzi Run `?read.maf` in R console. Change the option to what you want to analyze.
For tcga data, you can use TCGAbiolinks. A solution for your error is manually set the `vc_nonSyn` to all mutation types in the `read.maf`.
```r library(maftools) laml.maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools") #MAF file laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') #clinical data laml = read.maf(maf = laml.maf, clinicalData = laml.clin, vc_nonSyn =...
If it is truly important, maybe we can consider providing GisticCompare for two or more gistic objects. It should make sense.
The `other calculation` and `effect of CNV` are unclear here. If you can obtain what you want in `gene.summary`, why are you looking for other calculations?
What's the content of variable `hg38`?
Could you try running with `read.maf("var.annovar.maf", "clinical_data.tsv")` and also posting your session information? @shhabnsbwjd
@shhabnsbwjd Try `dir()`, you may find the file does not exist as @PoisonAlien pointed out. You need to locate your file and set the full path to it, or you...