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scar_score() with allele-specific segmentation file fails with Error in [.data.frame
(seg, , 8) : undefined columns selected
#7
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One add on: sample_name chromosome segment_start segment_end tcn nA nB ploidy I get:
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scar_score processes one sample each time. |
I did the following:
This is the described input format for HRDscore:
1st column: sample name,
2nd column: chromosome,
3rd column: segmentation start,
4th column: segmentation end,
5th column: total copynumber,
6th column: copy number of A allele,
7th column: copy number of B allele
However in the downstream processing what you need is the same order as in the original method for SNP6 Ascat output:
1: sample id
2: chromosome (numeric)
3: segment start
4: segment end
5: number of probes
6: total copy number
7: nA
8: nB
9: ploidy
10: contamination, aberrant cell fraction
That worked for me
Von: zhjianli <[email protected]>
Gesendet: Dienstag, 26. Januar 2021 03:35
An: sztup/scarHRD <[email protected]>
Cc: Thomas Grombacher <[email protected]>; Mention <[email protected]>
Betreff: Re: [sztup/scarHRD] scar_score() with allele-specific segmentation file fails with Error in `[.data.frame`(seg, , 8) : undefined columns selected (#7)
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@ThomasGro<https://github.com/ThomasGro> I had exactly the same issue. Did you solve the problem eventually? Thanks.
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I had exactly the same issue. Did you solve the problem eventually? Thanks. |
Please look at my comment from Jan 26th. |
Did this work correctly? I think their test file only has 8 columns with "ploidy" in the end |
Hi,
I have generated a allele-specific segmentation file with CNVkit. I adapted the format to fit your input
"... allele-specific segmentation file with the following columns: 1st column: sample name, 2nd column: chromosome, 3rd column: segmentation start, 4th column: segmentation end, 5th column: total copynumber, 6th column: copy number of A allele, 7th column: copy number of B allele"
sample_name chromosome segment_start segment_end tcn nA nB
model1 1 62676830 62677251 30 19 11
model1 1 173836085 177898343 3 2 1
model1 2 677597 1217588 5 4 1
But I get the error:
It seems the function is expecting an additional column?!
Thank you for your support,
Thomas
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