maftools

maftools copied to clipboard

vafCompare issue

3

Hi PoissonAlien, I constantly get an error message when using vafCompare on my own set of mutational samples. I've tried it on the TCGA studies as below, get the same...

NewBee100

**Describe the issue** Hi, i am confused about the "RNA" in Variant_Classification field, can you please tell me what does it mean and how it be generated?

jadonWong

I want to calculate TMB in gene level, which means that each gene has a corresponding tmb. I want to konw how to do it by maftools

DM0815

maftool package: No non-synonymous mutations found Check `vc_nonSyn`` argumet in `read.maf` for details

8

I have download the SNV data from TCGA database. But this error was reported when a maf file was read by read.maf command. So what's the meaning of that? How...

celluq

**Describe the issue** Hi, "Multi-hit" label is included in Oncoplot legend by default even though my data do not include samples with more than one variant and thus the representation...

espelpz

annovarToMaf

3

**Describe the issue** Hi I am trying to read in a dataset annotated by ANNOVAR, and the total number or rows should be 14841, however, it turned out to be...

xiw588

Subset genes in the initial steps

5

Is there a way to subset genes and remove some of them (namely) from the maf file? Or, the opposite, only keep the ones we want to investigate more and...

camcecc

Reading Clinical data with maftool

7

Hello, I want to read my clinical data using maf tools. The data is in tsv format and I am reading it using the code; read.maf(maf = "var.annovar.maf", clinicalData =...

shhabnsbwjd

Hi, I got the following warning message while plotting plotmafSummary. And I am only getting the SNP variant plot in the graph. Please help me with this issue. plotmafSummary(maf=oc, rmOutlier...

sinumol

Annovar to MAF question

7

Good Morning, I am relative new to the world of bioinformatics, I have been trying to convert annovar annotated files to maf, however it seems that there is problem in...

AsanchezMD