Genotype is not available at position # ######## about quantumclone HOT 14 CLOSED

Hi Charlotte,

First thing, contamination should be between 0 and 1, so using a contamination of 0.3 would reduce the number of variants rejected due to normalization issues.
Second, could you please check that the genotype is not -1 around your position (the line with the Start strictly lower to the variant you are looking at)?

Best wishes,
Paul

from quantumclone.

Hi Paul,

Yes indeed, I made a mistake contamination value when I wrote the issue (I noticed as soon as I posted the comment). I actually tested contamination = 0 when I tried to run QuantumClone.

When I check the genotype of the 6 variants detected, I got for instance A, and for UncertaintyOfGT I got -1 :

SNV file

  SampleName Chr   Start Depth Alt
1 sample1   1  909419    16   3
2 sample1   1  986894    20   2
3 sample1   1 1262354    95   3
4 sample1   1 1563476    73   2
5 sample1   1 1585590   117   2
6 sample1   1 1654193   247   3

CNV file

Chromosome	Start	Ratio	MedianRatio	CopyNumber	BAF	estimatedBAF	Genotype	UncertaintyOfGT	Gene
1	909213	0.505172	0.508169	1	1	1	A	-1	1: 909212- 909431
1	986833	0.593654	0.508169	1	-1	1	A	-1	1: 986832- 987025
1	1262621	0.599795	0.508169	1	-1	1	A	-1	1: 1262620- 1263143
1	1563399	0.566113	0.508169	1	1	1	A	-1	1: 1563398- 1563559
1	1585560	0.660535	0.508169	1	1	1	A	-1	1: 1585559- 1585739
1	1654147	0.996888	0.508169	1	-1	1	A	-1	1: 1654146- 1654257

Do you have an idea of what I should do to make it work?

Kind Regards,
-Charlotte

from quantumclone.

Hi Charlotte,

To prevent any delay in your work, I think the quickest would be to insert the genotype directly in your SNV table.
I'll try to fix the FREEC concatenation as soon as I can using the data you provided, but it may not be before next week.

Best wishes,
Paul

from quantumclone.

Hi Paul,

Thank you for your answer and your help.
I'll add the genotype in the SNV table in the meantime.

Kind Regards,
-Charlotte

from quantumclone.

Hi Charlotte,

The QuantumClone version 1.0.0.7 available on Github should fix your issue.

Best wishes,
Paul

from quantumclone.

Hi Paul,
Thanks for your doing it so quickly.
Unfortunately I have a new error now :

Checking that SNV_list and FREEC_list have the same number of samples...
Passed
epsilon set to: 0.00566125684264668
Checking all possibilities for <my sample>
Error in `[.data.frame`(z, as.character(z[, "Chromosome"]) == as.character(chr[i])) : 
  undefined columns selected

I tried different things to fix it, including renaming columns but errors are persisting, do you know where this problem comes from?

-Charlotte

from quantumclone.

Hi Charlotte,

Not having any FREEC file example, I worked on your extract, and used the first line as header. Could you check that there is a "Chromosome" column name?

Best wishes,
Paul

from quantumclone.

Hi Paul,

I'm using the same file, and the column name is "Chromosome" indeed:

> colnames(CNV_file)
 [1] "Chromosome"      "Start"           "Ratio"           "MedianRatio"     "CopyNumber"     
 [6] "BAF"             "estimatedBAF"    "Genotype"        "UncertaintyOfGT" "Gene"   

> head(CNV_file$Chromosome)
[1] 1 1 1 1 1 1
Levels: 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 X

> mode(CNV_file$Chromosome)
[1] "numeric"

Thank you again for your help,

Kind regards
-Charlotte

from quantumclone.

Hi Charlotte,

I tried a quick fix, tell me if it works (current version on Github).

Paul

from quantumclone.

Hi Paul,

Still not working, I've got something slightly different :

Error in `[.data.frame`(z, as.character(z[, ChrCol]) == as.character(chr[i])) : 
  undefined columns selected

-Charlotte

from quantumclone.

Hi Charlotte,

It seems that object received by the function is not a data.frame anymore. Are you still passing FREEC_list = FREEC_liste as argument or FREEC_list = CNV_file?

Best wishes,
Paul

from quantumclone.

Hi Paul,

I'm still passing

SNV_liste = list(SNV_file)
FREEC_liste = list(CNV_file)
contamination = 0
One_step_clustering(SNV_list = SNV_liste, FREEC_list = FREEC_liste, contamination, nclone_range = 2:5, clone_priors = NULL, prior_weight = NULL, Initializations = 1, preclustering = "FLASH", simulated = FALSE, epsilon = NULL, save_plot = TRUE, ncores = 1, restrict.to.AB = FALSE, output_directory = NULL, model.selection = "BIC", optim = "default", keep.all.models = FALSE, force.single.copy = FALSE)

Then I tried FREEC_list = CNV_file just in case but it's not working.

Kind regards,

-Charlotte

from quantumclone.

Hi Charlotte,

I have been trying to reproduce your error using your file, but to no avail. I cannot figure out what triggers your error as it works on my computer.
Unless you can provide me with a reproducible example, I'll mark this as closed.

Paul

from quantumclone.

Hi Paul,
I sent you an email last week with my input files and the complete script I used at quantumclone.package at gmail.com
Thank you for your help and your time,
Best
-Charlotte

from quantumclone.