Update whichSignatures.R

[ljl-suosi]

SP107141_sub_data.txt
For some cases, such as the SP107141 sample mutation data I've uploaded, after "default" normalization norm.mut.counts <- mut.counts/rowSums(mut.counts), the code round(rowSums(tumor), digits = 1) != 1 will be TRUE.

[raerose01]

Hi, sorry for the delay. Could you send the code you've run that generates an error? I tried the following and got an output ok.

test <- read.table("~/Downloads/SP107141_sub_data.txt", header = TRUE, stringsAsFactors = FALSE, check.names = FALSE)
boop <- whichSignatures(test, contexts.needed = TRUE)

Just want to make sure I understand what's going on.

Thanks,

Rachel

[ljl-suosi]

Yes, it works well on local computer. But on linux server, when I run the example data with the following codes

test <- read.table("~/Downloads/SP107141_sub_data.txt", header = TRUE, stringsAsFactors = FALSE, check.names = FALSE)
rownames(test) <- 'SP107141'
boop <- whichSignatures(test, contexts.needed = TRUE)

I got errors:

Error in whichSignatures(test, contexts.needed = TRUE) : 
  Sample:  SP107141  is not normalized
 Consider using "contexts.needed = TRUE"

By the way, here is my environment:

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          4                           
minor          0.2                         
year           2020                        
month          06                          
day            22                          
svn rev        78730                       
language       R                           
version.string R version 4.0.2 (2020-06-22)
nickname       Taking Off Again