trinucleotideMatrix

[Macy-Zhao]

Hi,
Resently, I used extractSignatures to get signatures,but it alway reported bug as below.
So, how could I can deal with this bug?
Thank you very much for replying!
Timing stopped at: 1635 856.7 351.6 Error in str_out(i) : object 'i' not found Calls: extractSignatures ... anyStrings -> isTRUE -> validityMethod -> paste -> str_out In addition: Warning messages: 1: In cor(d.consensus, d.coph, method = "pearson") : the standard deviation is zero 2: In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, : scheduled core 3 did not deliver a result, all values of the job will be affected 3: In (function (...) : NAs were produced due to errors in some of the runs: -#2[r=2] -> (list) object cannot be coerced to type 'double' [in call to 'which.min'] Execution halted

[ShixiangWang]

please run library(NMF) firstly and see if it works.

[Macy-Zhao]

I did ,but still presented this bug!

[PoisonAlien]

Hi,
It appears your matrix is malformed.

1. Try to run extractSignatures with pConstant = 0.1
2. If above doesn't work can you share your output from trinucleotideMatrix as an Rds file?

[Macy-Zhao]

Well done! Then I have another problem, that is the genes on the picture which is from plotEnrichmentResults are overlap with the number of samples,and it's hard to see which gene clearly. I'm sure no parameter to control, so How to solve this problem ? In addition,how could you add ylab and which means is y-axis?

[PoisonAlien]

Hi,
Sorry for the late reply. Its hard to imagine the issue, Is it possible to post a png of the image?

[Macy-Zhao]

the issue is the position indicated by the arrow on this image, the gene is covered by the number. Another problem is I don't know how I can add ylab on this image ?
How could I do?

[PoisonAlien]

Hi,
You can save the plot to some high res pdf and it should be okay. Or you can use annoFontSize and geneFontSize argument to control font sizes.

Regarding the label, once you run the above function use mtext to add labels to the existing plot.

plotEnrichmentResults(enrich_res = fab.ce, pVal = 0.05)
mtext(text = "Fraction", side = 2, las = 3, line = 2)

Hope this helps. Let me know if you have any followup questions.

[Macy-Zhao]

Thank you very much! I think it is not res pdf problem,maybe y-value of the position of genes is a little lower, if put gene name on the y-value of more than 1 that looks perfectly?
Will you consider annotation of p-value below each gene, such as the star and dot presents the p-value like this picture as below?

Another question is about pancanComparison, I use this function to get the different genes, but I aslo need know which mutation site information on this gene is different, and pvalue and FDR. how do I import the file that the gene is instead of mutation infor as below ?

[Tinalxt]

Hi,
It appears your matrix is malformed.

1. Try to run extractSignatures with pConstant = 0.1
2. If above doesn't work can you share your output from trinucleotideMatrix as an Rds file?

Hi,
I had the same wrong message when used the extractSignatures function.
I have no idea what's wrong with my data.
How could I can deal with this bug?
here is my data in Rds:
laml_tnm.zip

`laml.sign = estimateSignatures(mat = laml.tnm, nTry = 6, pConstant = 0.1)
-Running NMF for 6 ranks
Compute NMF rank= 2 ... Timing stopped at: 0 0 0.005
ERROR
Compute NMF rank= 3 ... Timing stopped at: 0 0 0.006
ERROR
Compute NMF rank= 4 ... Timing stopped at: 0.004 0 0.005

ERROR
Compute NMF rank= 5 ... Timing stopped at: 0 0.004 0.006
ERROR
Compute NMF rank= 6 ... Timing stopped at: 0 0.004 0.005
ERROR
Error in (function (...) : All the runs produced an error:
-#1 [r=2] -> Error: memory could not be allocated for instance of type big.matrix [in call to 'big.matrix']
-#2 [r=3] -> Error: memory could not be allocated for instance of type big.matrix [in call to 'big.matrix']
-#3 [r=4] -> Error: memory could not be allocated for instance of type big.matrix [in call to 'big.matrix']
-#4 [r=5] -> Error: memory could not be allocated for instance of type big.matrix [in call to 'big.matrix']
-#5 [r=6] -> Error: memory could not be allocated for instance of type big.matrix [in call to 'big.matrix']
`

[ShixiangWang]

@Tinalxt Do you use the latest version of maftools? I don't find any problem. Do you run library(NMF) firstly?

> test = readRDS("~/Downloads/laml_tnm")
> library(NMF)
载入需要的程辑包：pkgmaker
载入需要的程辑包：registry

载入程辑包：‘pkgmaker’

The following object is masked from ‘package:base’:

    isFALSE

载入需要的程辑包：rngtools
载入需要的程辑包：cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 7/8
  To enable shared memory capabilities, try: install.extras('
NMF
')
> library(maftools)
> res = extractSignatures(test, n = 3)
-Running NMF for factorization rank: 3
-Finished in0.859s elapsed (0.837s cpu)







> devtools::session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.1 (2019-07-05)
 os       macOS High Sierra 10.13.6   
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  zh_CN.UTF-8                 
 ctype    zh_CN.UTF-8                 
 tz       Asia/Shanghai               
 date     2019-12-25                  

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package      * version    date       lib source                            
 assertthat     0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                    
 backports      1.1.5      2019-10-02 [1] CRAN (R 3.6.0)                    
 bibtex         0.4.2      2017-06-30 [1] CRAN (R 3.6.0)                    
 Biobase      * 2.46.0     2019-10-29 [1] Bioconductor                      
 BiocGenerics * 0.32.0     2019-10-29 [1] Bioconductor                      
 callr          3.4.0      2019-12-09 [1] CRAN (R 3.6.0)                    
 cli            2.0.0      2019-12-09 [1] CRAN (R 3.6.0)                    
 cluster      * 2.1.0      2019-06-19 [2] CRAN (R 3.6.1)                    
 codetools      0.2-16     2018-12-24 [2] CRAN (R 3.6.1)                    
 colorspace     1.4-1      2019-03-18 [1] CRAN (R 3.6.0)                    
 crayon         1.3.4      2017-09-16 [1] CRAN (R 3.6.0)                    
 data.table     1.12.8     2019-12-09 [1] CRAN (R 3.6.0)                    
 desc           1.2.0      2018-05-01 [1] CRAN (R 3.6.0)                    
 devtools       2.2.1      2019-09-24 [1] CRAN (R 3.6.0)                    
 digest         0.6.23     2019-11-23 [1] CRAN (R 3.6.0)                    
 dlstats        0.1.3      2019-11-14 [1] CRAN (R 3.6.0)                    
 doParallel     1.0.15     2019-08-02 [1] CRAN (R 3.6.0)                    
 dplyr          0.8.3      2019-07-04 [1] CRAN (R 3.6.0)                    
 ellipsis       0.3.0      2019-09-20 [1] CRAN (R 3.6.0)                    
 fansi          0.4.0      2018-10-05 [1] CRAN (R 3.6.0)                    
 foreach        1.4.7      2019-07-27 [1] CRAN (R 3.6.0)                    
 fs             1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                    
 ggplot2        3.2.1.9000 2019-12-19 [1] Github (tidyverse/ggplot2@351eb41)
 glue           1.3.1      2019-03-12 [1] CRAN (R 3.6.0)                    
 gridBase       0.4-7      2014-02-24 [1] CRAN (R 3.6.0)                    
 gtable         0.3.0      2019-03-25 [1] CRAN (R 3.6.0)                    
 iterators      1.0.12     2019-07-26 [1] CRAN (R 3.6.0)                    
 jsonlite       1.6        2018-12-07 [1] CRAN (R 3.6.0)                    
 lattice        0.20-38    2018-11-04 [2] CRAN (R 3.6.1)                    
 lifecycle      0.1.0      2019-08-01 [1] CRAN (R 3.6.0)                    
 maftools     * 2.2.10     2019-12-16 [1] Bioconductor                      
 magrittr       1.5        2014-11-22 [1] CRAN (R 3.6.0)                    
 Matrix         1.2-18     2019-11-27 [2] CRAN (R 3.6.0)                    
 memoise        1.1.0      2017-04-21 [1] CRAN (R 3.6.0)                    
 munsell        0.5.0      2018-06-12 [1] CRAN (R 3.6.0)                    
 NMF          * 0.21.0     2018-03-06 [1] CRAN (R 3.6.0)                    
 packrat        0.5.0      2018-11-14 [1] CRAN (R 3.6.0)                    
 pacman       * 0.5.1      2019-03-11 [1] CRAN (R 3.6.0)                    
 pillar         1.4.2      2019-06-29 [1] CRAN (R 3.6.0)                    
 pkgbuild       1.0.6      2019-10-09 [1] CRAN (R 3.6.0)                    
 pkgconfig      2.0.3      2019-09-22 [1] CRAN (R 3.6.0)                    
 pkgload        1.0.2      2018-10-29 [1] CRAN (R 3.6.0)                    
 pkgmaker     * 0.27       2018-05-25 [1] CRAN (R 3.6.0)                    
 plyr           1.8.5      2019-12-10 [1] CRAN (R 3.6.0)                    
 prettyunits    1.0.2      2015-07-13 [1] CRAN (R 3.6.0)                    
 processx       3.4.1      2019-07-18 [1] CRAN (R 3.6.0)                    
 ps             1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                    
 purrr          0.3.3      2019-10-18 [1] CRAN (R 3.6.0)                    
 R6             2.4.1      2019-11-12 [1] CRAN (R 3.6.0)                    
 RColorBrewer   1.1-2      2014-12-07 [1] CRAN (R 3.6.0)                    
 Rcpp           1.0.3      2019-11-08 [1] CRAN (R 3.6.0)                    
 registry     * 0.5-1      2019-03-05 [1] CRAN (R 3.6.0)                    
 remotes        2.1.0      2019-06-24 [1] CRAN (R 3.6.0)                    
 reshape2       1.4.3      2017-12-11 [1] CRAN (R 3.6.0)                    
 rlang          0.4.2      2019-11-23 [1] CRAN (R 3.6.0)                    
 rngtools     * 1.4        2019-07-01 [1] CRAN (R 3.6.0)                    
 rprojroot      1.3-2      2018-01-03 [1] CRAN (R 3.6.0)                    
 rstudioapi     0.10       2019-03-19 [1] CRAN (R 3.6.0)                    
 scales         1.1.0      2019-11-18 [1] CRAN (R 3.6.0)                    
 sessioninfo    1.1.1      2018-11-05 [1] CRAN (R 3.6.0)                    
 stringi        1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                    
 stringr        1.4.0      2019-02-10 [1] CRAN (R 3.6.0)                    
 survival       3.1-8      2019-12-03 [2] CRAN (R 3.6.0)                    
 testthat       2.3.1      2019-12-01 [1] CRAN (R 3.6.0)                    
 tibble         2.1.3      2019-06-06 [1] CRAN (R 3.6.0)                    
 tidyselect     0.2.5      2018-10-11 [1] CRAN (R 3.6.0)                    
 usethis        1.5.1      2019-07-04 [1] CRAN (R 3.6.0)                    
 withr          2.1.2      2018-03-15 [1] CRAN (R 3.6.0)                    
 wordcloud      2.6        2018-08-24 [1] CRAN (R 3.6.0)                    
 xtable         1.8-4      2019-04-21 [1] CRAN (R 3.6.0)                    

[1] /Users/wsx/R_library
[2] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

[ShixiangWang]

@PoisonAlien This issue is inactive and should be closed. I can't see a reason to make it open :).