search

griffithlab / GenVisR

Genome data visualizations
Creative Commons Zero v1.0 Universal
206 stars 62 forks source link

cnFreq did not detect identical genomic segments for all patients #360

Open hannaeng opened 5 years ago

hannaeng commented 5 years ago

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: image

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 commented 5 years ago

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 commented 5 years ago

Hi Zachary,

Thank you for the clue! All my columns were factors…

Kind regards, Hanna


Hanna Engqvist, PhD student
hanna.engqvist@gu.se<mailto:hanna.engqvist@gu.se>
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:notifications@github.com]
Sent: Wednesday, May 29, 2019 5:17 PM
To: griffithlab/GenVisR <GenVisR@noreply.github.com>
Cc: Hanna Engqvist <hanna.engqvist@gu.se>; Author <author@noreply.github.com>
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<https://github.com/griffithlab/GenVisR/issues/360?email_source=notifications&email_token=AMF63SV5QRB6EJXX5WCWOSTPX2NALA5CNFSM4HQA32PKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWPVOZY#issuecomment-496981863>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AMF63SRU7RNCCUBYMVENVN3PX2NALANCNFSM4HQA32PA>.
youtruth commented 8 months ago

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 commented 8 months ago

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