no input.Rdata file when using each sample as their own control

[nstickle]

Hi, when I try running each sample as its own control I do not get an input.Rdata file and so cannot run plotCNA. Otherwise it appears to have worked correctly, I get the following files as output: bam file index for bam file peaks1.bed CopywriteR.log log2_read_counts.igv read_counts.txt

Any idea why? Thanks, Natalie

[nstickle]

I should have added that I got this error at the end:

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements

Thanks.

[thomasKuilman]

Hi Natalie,

I am quite sure this has something to use the optional capture-regions.file argument to specify a location for a bed file with peak locations. Is that correct? If so, you should double-check the format of the bed file. You get this error message when R tries to read a table, where in the first line you have a different number of ‘columns’ than in the rest of the file.

I hope that helps, otherwise let me know.

Best,

Thomas

---

Thomas Kuilman, PhD Department of Molecular Oncology & Immunology Netherlands Cancer Institute 1066 CX Amsterdam The Netherlands

Phone: +31-20-5121841

On 1 Mar 2018, at 23:26, nstickle notifications@github.com<mailto:notifications@github.com> wrote:

Hi, when I try running each sample as its own control I do not get an input.Rdata file and so cannot run plotCNA. Otherwise it appears to have worked correctly, I get the following files as output: bam file index for bam file peaks1.bed CopywriteR.log log2_read_counts.igv read_counts.txt

Any idea why? Thanks, Natalie

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[nstickle]

Thank you. I had that thought, and did think that I had checked that... but it does seem it was the problem, there was a header line in the bed file.

Natalie

[thomasKuilman]

Hi Nathalie,

I will leave the issue open on Github as I realized that in the bed format a track line is allowed, and hence CopywriteR should not choke on this. Hopefully I can implement that in the future.

Best regards,

Thomas

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On 8 Mar 2018, at 18:25, nstickle notifications@github.com<mailto:notifications@github.com> wrote:

Thank you. I had that thought, and did think that I had checked that... but it does seem it was the problem, there was a header line in the bed file.

Natalie

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