Error in iteration 2: arguments imply differing number of rows
royfrancis opened this issue · 2 comments
royfrancis commented
I am running SCEVAN like so:
library(SCEVAN)
dat <- readRDS("TN-B1-4031.rds")
SCEVAN::pipelineCNA(dat, sample = "TN-B1-4031", par_cores = 20, SUBCLONES = TRUE, plotTree = TRUE)
and it crashes with the following error:
Error in iteration 2: arguments imply differing number of rows: 0, 48
It only happens with some of my samples.
The data looks like this:
> dat[1:5,1:5]
pal_2021_GSM4909285_1-0 pal_2021_GSM4909285_2-0
UQCR10 8 4
SPP1 0 0
HLA-DPB1 0 0
B2M 14 12
RAB14 2 1
pal_2021_GSM4909285_3-0 pal_2021_GSM4909285_4-0
UQCR10 0 10
SPP1 0 0
HLA-DPB1 0 0
B2M 1 10
RAB14 0 2
pal_2021_GSM4909285_5-0
UQCR10 2
SPP1 0
HLA-DPB1 0
B2M 2
RAB14 2
The data file can be downloaded here. Here is another smaller dataset that fails.
Here is the full log:
Full log
[1] " raw data - genes: 13253 cells: 1482"
[1] "1) Filter: cells > 200 genes"
[1] "low data quality"
[1] "2) Filter: genes > 5% of cells"
[1] "2451 genes past filtering"
[1] "3) Annotations gene coordinates"
The number of elements of the gene set is less than the minimum allowed.
The number of elements of the gene set is less than the minimum allowed.
The number of elements of the gene set is less than the minimum allowed.
The number of elements of the gene set is less than the minimum allowed.
...
<This line is repeated hundreds of times>
...
The number of elements of the gene set is less than the minimum allowed.
The number of elements of the gene set is less than the minimum allowed.
The number of elements of the gene set is less than the minimum allowed.
The number of elements of the gene set is less than the minimum allowed.
[1] "found 30 confident non malignant cells"
[1] "2378 genes annotated"
[1] "4) Filter: genes involved in the cell cycle"
[1] "2205 genes past filtering "
[1] "5) Filter: cells > 5genes per chromosome "
[1] "6) Log Freeman Turkey transformation"
[1] "A total of 174 cells, 2205 genes after preprocessing"
[1] "7) Measuring baselines (confident normal cells)"
[1] "8) Smoothing data"
[1] "9) Segmentation (VegaMC)"
[1] "10) Adjust baseline"
[1] "11) plot heatmap"
[1] "found 48 tumor cells"
[1] "time classify tumor cells: 23.0540297031403"
[1] "found 2 subclones"
percentage_cells_subsclone_1 percentage_cells_subsclone_2
0.4166667 0.5833333
[1] "Segmentation of subclone : 1"
[1] "Segmentation of subclone : 2"
$`wu-2021_4465_subclone1`
Chr Start End Alteration segm.mean
2 1 16974502 31944856 -2 -0.215354
43 8 11795573 54147901 2 0.095991
46 8 97644179 144428563 2 0.122258
58 11 20363685 73761137 2 0.156543
63 12 752593 96269835 -2 -0.358043
68 12 112013316 123633766 2 0.159426
70 13 36998816 77019143 -2 -0.229887
71 13 95677139 114305817 -2 -0.238055
82 16 47154387 89968060 -2 -0.225194
85 17 7240014 57006768 -2 -0.301897
89 18 3247481 9285985 2 0.183345
91 18 56597208 80033949 2 0.137885
92 19 571277 4670370 2 0.048158
95 19 41956681 54194536 -2 -0.180862
98 20 44496221 63891545 -2 -0.201054
99 21 17593653 46665124 -2 -0.305551
13 2 177212563 197516737 -1 -0.064736
15 3 3148992 11771350 1 0.189506
16 3 13549131 48504826 -1 -0.062771
19 3 139517434 158829719 1 0.107402
47 9 121038 35732395 1 0.127720
80 16 4461680 24572863 1 0.186913
$`wu-2021_4465_subclone2`
Chr Start End Alteration segm.mean
4 1 150265399 167937040 2 0.244055
53 12 752593 14803540 -2 -0.254675
55 12 46358189 107713167 -2 -0.116435
58 13 19633681 114305817 -2 -0.121179
68 16 3018445 30085377 2 0.244846
2 1 19640554 39487177 -1 -0.140271
13 3 33798352 52239260 -1 -0.105971
28 6 30345131 33711727 -1 -0.044950
50 11 62433542 65862026 1 0.188088
$`wu-2021_4465_clone`
Chr Start End Alteration segm.mean
5 1 203795654 246768137 2 0.316165
10 2 264140 88750935 2 0.319686
14 2 201071433 241686991 2 0.236119
21 3 184174689 195584205 -2 -0.211273
22 4 1166932 155953917 -2 -0.238754
26 5 218241 55535050 2 0.193638
29 5 135570679 163519336 -2 -0.207735
34 6 42744481 169254044 2 0.213288
39 7 1152071 66958551 2 0.423589
49 9 99222064 137615360 -2 -0.269008
54 10 80131682 133373689 -2 -0.161538
56 11 307631 6619461 -2 -0.448406
61 11 102520508 134253370 -2 -0.088353
72 14 34981957 105480170 -2 -0.192639
75 15 24823637 58933653 -2 -0.194629
87 17 68035519 82730328 2 0.054674
93 19 5891276 17323301 -2 -0.202012
101 22 28794555 50628173 -2 -0.263656
Error in iteration 2: arguments imply differing number of rows: 0, 48
I have also tried reinstalling SCEVAN to the current version as of 8-Aug-2024.
R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
SCEVAN_1.0.1
AntonioDeFalco commented
Hi @royfrancis,
The error is due to the very low quality of the sample, in which only 2,451 genes pass the filters and the tumor fraction appears to be close to zero. Only 48 tumor cells were identified, so I don't recommend using the subclonal analysis I see from the log.
Thanks.
royfrancis commented
Thanks for looking into this! 🙏🏼 This was helpful feedback.