search

VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
162 stars 85 forks source link

Error in !is.null(homsegs) && !is.na(homsegs) : #166

Closed mital14 closed 6 months ago

mital14 commented 8 months ago

I have ASCAT v3.1.2 and have the issue [1] Plotting tumor data [1] Sample S1 (1/100) Error in !is.null(homsegs) && !is.na(homsegs) : 'length = 6' in coercion to 'logical(1)' Calls: ascat.aspcf Execution halted

zhangzhhcb commented 7 months ago

Hi, "homsegs" is the germline homozygous stretches. The error message indicates that no any homo segments was detected. Do you have normal control or you run the tumor only mode? You may need to check your normal sample.

tlesluyes commented 7 months ago

Hi @mital14,

This issue seems related to newer versions of R (4.3.0+) where arguments around the && operator must have the same lengths. A fix has been implemented as part of ASCAT v3.1.2 (https://github.com/VanLoo-lab/ascat/commit/c4c10f8bc5deecc0b0e18f46dd271934e554d73e) but we did not create a specific release for it. In your case, you must be using a v3.1.2 prior to this fix so installing a newer version of ASCAT (devtools::install_github('VanLoo-lab/ascat/ASCAT')) should fix your issue.

@zhangzhhcb: this dataset (S1 (1/100)) corresponds to the example dataset of 100 samples we provide here.

Cheers,

Tom.