Showing mutational load with a same scale

[beginner984]

Hello @PoisonAlien

I have two groups

Is there any way to show mutation per sample with the scale? I thought in combining two groups by showing barcode but I noticed patients are placed irregularly regardless of their own groups.

[PoisonAlien]

This would not be possible because they are cohort specific. But, If you want to show differences in mutation load you can use tmb

> par(mfrow = c(1, 2))
> tmb(maf = maf1)
> tmb(maf = maf2)

[MaryGoAround]

Sorry, given two maf objects what you mean by tab

> par(mfrow = c(1, 2))
> tmb(maf = maf1)
Error in tmb(maf = maf1) : could not find function "tmb"

You mean oncoplot?

[PoisonAlien]

You will have to update the package for this function.

[beginner984]

Excuse me @PoisonAlien, by

tmb(maf = laml,captureSize = 50,logScale = FALSE) I see Median : 1.84/mb, does this mean that 1.84 per each 50 mega bases of the genome because captureSize = 50?

When I put captureSize = 1, I get this

Because I am working on a cancer for which a reference paper has been published in which says median was 6.4 such mutations per mega base , that is why I worry I may I calculate TMB wrong that I see TMB as 1.84

[PoisonAlien]

Capture size indicates the size of genome that is sequenced. For example exome-seq with Agilent sureselect kit captures ~50mb of the genome. If you observe 100 mutations then your TMB is 100/50 = 2per mb. Probably there are more fancier ways to estimate TMB but here its just a simple division with capture size.

[beginner984]

Sorry @PoisonAlien

I have to groups of patients for them I plotted mutational burden like this

My boss says I should find a way to make Y axis at the same scale I mean by bared eyes we can see the differences, for example looking at y axis one group crosses the 0 while another one is 0.5

Is there any possible change to the function can to this?

[PoisonAlien]

No its not possible.

[beginner984]

Sorry @PoisonAlien

Total mutation burden in my samples is like

> tmb
    Tumor_Sample_Barcode total total_perMB total_perMB_log
 1:    LP6008202-DNA_B03     7        0.14    -0.853871964
 2:    LP6008460-DNA_F02    49        0.98    -0.008773924
 3:                  s59    55        1.10     0.041392685

I did not figure out what is the difference of total and total_perMB

For instance for LP6008202-DNA_B03 totalis 7 but by mafSummary , ms$variant.classification.summary total is 4395

Please you may help me of these definitions

Thank you

[PoisonAlien]

Can you post the below output?

getSampleSummary(ms)[Tumor_Sample_Barcode %in% c("LP6008202-DNA_B03", "LP6008460-DNA_F02", "s59")]

total is the number of variants (excluding CNVs, and syn mutations) in a sample.

[beginner984]

Thank you

> getSampleSummary(ms)[Tumor_Sample_Barcode %in% c("LP6008202-DNA_B03", "LP6008460-DNA_F02", "s59")]
   Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins
1:                  s59               1               2            2            0
2:    LP6008460-DNA_F02               1               1            1            1
3:    LP6008202-DNA_B03               0               0            0            0
   Missense_Mutation Nonsense_Mutation Nonstop_Mutation Splice_Site total
1:                48                 2                0           0    55
2:                39                 3                1           2    49
3:                 7                 0                0           0     7
> 
> 

[PoisonAlien]

Seems ok to me.