rainfallPlot ignore mutations in X and Y chromosomes? about maftools

[PoisonAlien]

Hi,
No it doesn't remove X and Y chromosomes. All 24 (22 + XY) chromosomes are plotted. How are chromosome X and Y are labelled in MAF ?

For change-point, I must admit that its not a robust method ! It will detect any genomic loci where inter-event distance changes. For e.g, in case of chromosome 4, the detected changepoint at the center, that is where mutation burden is higher compared to beginning of chromosome. See #13 for more. I am also thinking of removing this option in future update.

[crazyhottommy]

update.: OPs...I think something was wrong when I merged maf files.

X and Y are present in each maf files, but after merging, some NA was produced.
I removed header for each maf first and then used cat *maf > merged.maf and then add the header later.

How do you merge maf files? I used vcf2maf to get the maf files.

It is labeled as X and Y. I check the maf files under unix:

less my.maf | cut -f5 | sort | uniq -c
   1 "Chromosome"
10457 1
5337 10
6939 11
7069 12
5875 13
4881 14
3578 15
2957 16
2840 17
4430 18
2221 19
12185 2
2725 20
2007 21
1121 22
9601 3
9222 4
7765 5
8722 6
8333 7
8013 8
5885 9
4091 NA

I also checked the maf object after reading into maftools;

my.maf@data %>% group_by(Chromosome) %>% summarise(cnt = n()) %>% print(n=23)
# A tibble: 23 × 2
   Chromosome   cnt
        <int> <int>
1           1 10457
2           2 12185
3           3  9601
4           4  9222
5           5  7765
6           6  8722
7           7  8333
8           8  8013
9           9  5885
10         10  5337
11         11  6939
12         12  7069
13         13  5875
14         14  4881
15         15  3578
16         16  2957
17         17  2840
18         18  4430
19         19  2221
20         20  2725
21         21  2007
22         22  1121
23         NA  4091

I do not see X and Y.

[crazyhottommy]

I fixed the merged maf, but still no points showing in the X and Y for the rainfall plot.

 cat merged.maf | cut -f5 | sort | uniq -c
10457 1
5337 10
6939 11
7069 12
5875 13
4881 14
3578 15
2957 16
2840 17
4430 18
2221 19
12185 2
2725 20
2007 21
1121 22
9601 3
9222 4
7765 5
8722 6
8333 7
8013 8
5885 9
   1 Chromosome
   2 MT
3709 X
 380 Y

my.maf@data %>% group_by(Chromosome) %>% summarise(cnt = n()) %>% print(n=25)
# A tibble: 25 × 2
   Chromosome   cnt
        <chr> <int>
1           1 10457
2          10  5337
3          11  6939
4          12  7069
5          13  5875
6          14  4881
7          15  3578
8          16  2957
9          17  2840
10         18  4430
11         19  2221
12          2 12185
13         20  2725
14         21  2007
15         22  1121
16          3  9601
17          4  9222
18          5  7765
19          6  8722
20          7  8333
21          8  8013
22          9  5885
23         MT     2
24          X  3709
25          Y   380

[PoisonAlien]

Ahh ! I found the culprit. While tranforming segments into linearized scale, I forgot to convert chrX and chrY to 23 and 24. I will fix it soon !
Meanwhile, sorry to ask, but can you change X, Y to 23, 24 in your MAF and try ? It should work.

[crazyhottommy]

I downloaded the dev branch of maftools, the problem is still there.

[PoisonAlien]

ohh ! that is odd. Wait let me see..

[PoisonAlien]

Hi Tommy,
I am not able to reproduce this on a similar maf with same chromosome name as yours. Can you share the data for above sample ?