scar_score() with allele-specific segmentation file fails with Error in `[.data.frame`(seg, , 8) : undefined columns selected

[ThomasGro]

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:

scar_score("./x.tsv", reference = "grch37") Error in [.data.frame(seg, , 8) : undefined columns selected

It seems the function is expecting an additional column?!

Thank you for your support, Thomas

[ThomasGro]

One add on: when I add another column wioth ploidy information as in your example file:

sample_name chromosome segment_start segment_end tcn nA nB ploidy model1 1 62676830 62677251 30 19 11 2 model1 1 173836085 177898343 3 2 1 2 model1 2 677597 1217588 5 4 1 2

I get:

scar_score("./x.tsv", reference = "grch37") Determining HRD-LOH, LST, TAI Error in write.table(t(HRDresulst), paste0(outputdir, "/", run_name, "_HRDresults.txt"), : invalid 'row.names' specification

[zhjianli]

scar_score processes one sample each time.

[ThomasGro]

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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@ThomasGrohttps://github.com/ThomasGro I had exactly the same issue. Did you solve the problem eventually? Thanks.

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[sheny-bio]

I had exactly the same issue. Did you solve the problem eventually? Thanks.

[ThomasGro]

Please look at my comment from Jan 26th. You have to reorder the columns of the input table - at least that worked for me.

[jwuatx]

5: number of probes

Did this work correctly? I think their test file only has 8 columns with "ploidy" in the end