maftools

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

1

**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...

FriederikeHanssen

How to calculate the p-value between the mutation profiles for the 3 groups

1


sjb-a11y

No non-synonymous mutations found

1

Hi first of all thanks for this great tool! I am trying to read my .maf file but I want classify all the mutations as non-silent because I need all...

aeozdemr

selectedPathways argument in oncoplot not functioning properly with user-defined pathways

3

Hi, I'm having an issue with the "selectedPathways" argument in the oncoplot function, when using my own user-defined pathways. I either get the error below (with code): ``` oncoplot(maf =...

kbrar4013

The variants are almost Silent

1

Hi, When I use read.maf to read maf file, but almost variants are silent(silent variants/all variants: **16874**/17013). I am unsure about that is annotation problem or something. `df = read.maf('filter.vep.maf')`...

DayTimeMouse

Error applying colors to continuous clinicalFeatures

10

**Describe the issue** Hello, I am having an issue trying to add continuous clinical features to my oncoplot. If I add more than one clinicalFeature that has continuous values the...

juferban

Cannot find function Oncogenic Pathways

1

**Describe the issue** Hello! I am using maftools version 2.21.1 and am not able to use the function OncogenicPathways. I saw some documentation online that this function may only exist...

londonlondon20

sampleSwaps Error: Zero SNPs to analyze

1

Hi, Thank you for developing this very useful package. I was trying to run the sampleSwaps command to check whether my bam files belong to the same cases. But while...

tc86

Error:long vectors not supported yet: memory.c:3940

1

Hi, While running this `laml.tnm = trinucleotideMatrix(maf = combined_maf, prefix = 'chr', add = TRUE, ref_genome = "BSgenome.Hsapiens.UCSC.hg18")` , I got a mistake, like ``` Warning in trinucleotideMatrix(maf = combined_maf,...

Olsennnnn

Questions of GISTIC and copy number alteration analysis

1

**Describe the issue** Hi I am planning to analyze copy number alterations in a small cohort (n=15), and I have the segmentation data in TCGA format. I tried to generate...

xiw588