cnFreq did not detect identical genomic segments for all patients

[hannaeng]

Hi,

I am trying to construct frequency plots for copy number data using cnFreq but I received an error message saying the following:

#load data
CNdata <- read.delim("cnFreq_CN data (91 patients).txt", header=FALSE)
colnames(CNdata) <- c("chromosome", "start", "end", "segmean", "sample")
#call the cnFreq function
cnFreq(CNdata, genome="hg38")
Did not detect identical genomic segments for all samples ...Performing disjoin operation
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
solving row 1: range cannot be determined from the supplied arguments (too many NAs)
In addition: Warning messages:
1: In cnFreq_qual(x) : NAs introduced by coercion
2: In cnFreq_qual(x) : NAs introduced by coercion
3: In cnFreq_qual(x) : NAs introduced by coercion

My input file:

I am using GenVisR v. 1.16.0.

Is it also possible to stratify patients according to different groups and to create frequency plots for the same?

Thank you for your help.

Kind regards,
Hanna

[zlskidmore]

Hi Hanna,

Can you send me the output of str() on your data frame? I suspect a column, maybe start or end is not numeric?

[hannaeng]

Hi Zachary, Thank you for the clue! All my columns were factors… Kind regards, Hanna ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Hanna Engqvist, PhD student [email protected]<mailto:[email protected]> Sahlgrenska Academy at University of Gothenburg Institute of Clinical Sciences Department of Oncology Tel: (+46) 31 7866751 Physical address: Sahlgrenska Cancer Center Medicinaregatan 1G, 6th floor SE-413 90 Gothenburg, Sweden Mailing address: Sahlgrenska Cancer Center University of Gothenburg Box 425 SE-405 30 Gothenburg, Sweden From: Zachary Skidmore [mailto:[email protected]] Sent: Wednesday, May 29, 2019 5:17 PM To: griffithlab/GenVisR <[email protected]> Cc: Hanna Engqvist <[email protected]>; Author <[email protected]> Subject: Re: [griffithlab/GenVisR] cnFreq did not detect identical genomic segments for all patients (#360) Hi Hanna, Can you send me the output of str() on your data frame? I suspect a column, maybe start or end is not numeric? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#360?email_source=notifications&email_token=AMF63SV5QRB6EJXX5WCWOSTPX2NALA5CNFSM4HQA32PKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWPVOZY#issuecomment-496981863>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AMF63SRU7RNCCUBYMVENVN3PX2NALANCNFSM4HQA32PA>.

[youtruth]

Hi Hanna,

Can you send me the output of str() on your data frame? I suspect a column, maybe start or end is not numeric?

Could I also hear an answer to this error? I'm in a similar situation and curious about how it was resolved.

[zlskidmore]

I recall a issue recently where the input contained the same sample repeated, GenVisR does not perform this type of QC check. Can you test this? Otherwise to debug try just two samples and see if it still errors