Broken CLI : runIchorCNA.R: line 50: Syntaxerror

[sroener]

Hi,

I have been updating my ichorCNA version and now I get the following error:

runIchorCNA.R: line 50: Syntaxerror at unexpected word `('
runIchorCNA.R: line 50: `run_ichorCNA <- function(tumor_wig, normal_wig = NULL, gcWig, mapWig, repTimeWig, normal_panel=NULL, sex = NULL, exons.bed=NULL, id = "test", '

This happens both with the full command or just with runIchorCNA.r --help.

Full command:

runIchorCNA.R --id test19_processed --WIG results/testrun/icorCNA/readcounts/test19_index_processed.hg19.wig \
--ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5 \
--gcWig resources/ichorCNA/gc_hg19_1000kb.wig \
--mapWig resources/ichorCNA/map_hg19_1000kb.wig \
--centromere resources/ichorCNA/GRCh37.p13_centromere_UCSC-gapTable.txt \
--normalPanel resources/ichorCNA/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds \
--includeHOMD False \
--chrs 'c(1:22,"X")' \
 --chrTrain "c(1:22)" \
--estimateNormal True \
--estimatePloidy True \
--estimateScPrevalence True \
--scStates "c(1,3)" \
--txnE 0.9999 \
--txnStrength 10000 \
--plotFileType png \
--genomeBuild hg19 \
--genomeStyle UCSC \
--outDir results/testrun/icorCNA/test19_processed_hg19

ichorCNA was installed via bioconda:

name: ichorCNA
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - r-ichorcna
  - hmmcopy

The final environment looks like this:

 - _libgcc_mutex=0.1=conda_forge                                                                                                                                                                            
  - _openmp_mutex=4.5=2_gnu                                                                                                                                                                                  
  - _r-mutex=1.0.1=anacondar_1                                                                                                                                                                               
  - argcomplete=3.0.6=pyhd8ed1ab_0                                                                                                                                                                           
  - binutils_impl_linux-64=2.40=hf600244_0                                                                                                                                                                   
  - bioconductor-biobase=2.58.0=r42hc0cfd56_0                                                                                                                                                                
  - bioconductor-biocgenerics=0.44.0=r42hdfd78af_0                                                                                                                                                           
  - bioconductor-biocio=1.8.0=r42hdfd78af_0                                                                                                                                                                  
  - bioconductor-biocparallel=1.32.5=r42hc247a5b_0                                                                                                                                                           
  - bioconductor-biostrings=2.66.0=r42hc0cfd56_0                                                                                                                                                             
  - bioconductor-bsgenome=1.66.3=r42hdfd78af_0                                                                                                                                                               
  - bioconductor-bsgenome.hsapiens.ucsc.hg19=1.4.3=r42hdfd78af_6                                                                                                                                             
  - bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.5=r42hdfd78af_0                                                                                                                                             
  - bioconductor-data-packages=20230420=hdfd78af_0                                                                                                                                                           
  - bioconductor-delayedarray=0.24.0=r42hc0cfd56_0                                                                                                                                                           
  - bioconductor-genomeinfodb=1.34.9=r42hdfd78af_0                                                                                                                                                           
  - bioconductor-genomeinfodbdata=1.2.9=r42hdfd78af_0                                                                                                                                                        
  - bioconductor-genomicalignments=1.34.0=r42hc0cfd56_0                                                                                                                                                      
  - bioconductor-genomicranges=1.50.0=r42hc0cfd56_0                                                                                                                                                          
  - bioconductor-hmmcopy=1.40.0=r42hc0cfd56_0                                                                                                                                                                
  - bioconductor-iranges=2.32.0=r42hc0cfd56_0                                                                                                                                                                
  - bioconductor-matrixgenerics=1.10.0=r42hdfd78af_0                                                                                                                                                         
  - bioconductor-rhtslib=2.0.0=r42hc0cfd56_0                                                                                                                                                                 
  - bioconductor-rsamtools=2.14.0=r42hc247a5b_0                                                                                                                                                              
  - bioconductor-rtracklayer=1.58.0=r42h171f361_1                                                                                                                                                            
  - bioconductor-s4vectors=0.36.0=r42hc0cfd56_0                                                                                                                                                              
  - bioconductor-summarizedexperiment=1.28.0=r42hdfd78af_0                                                                                                                                                   
  - bioconductor-xvector=0.38.0=r42hc0cfd56_0                                                                                                                                                                
  - bioconductor-zlibbioc=1.44.0=r42hc0cfd56_0                                                                                                                                                               
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  - r-futile.options=1.0.1=r42hc72bb7e_1003                                                                                                                                                                  
  - r-getopt=1.20.3=r42ha770c72_3                                                                                                                                                                            
  - r-ggplot2=3.4.2=r42hc72bb7e_0                                                                                                                                                                            
  - r-glue=1.6.2=r42h06615bd_1                                                                                                                                                                               
  - r-gtable=0.3.3=r42hc72bb7e_0                                                                                                                                                                             
  - r-ichorcna=0.5.0=pl5321r42hdfd78af_0                                                                                                                                                                     
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Help would be appreciated!

[IanCodes]

I discovered this problem recently. I appears that the runIchorCNA.R file for v0.5.0 only contains the run_ichorCNA() function. This means it cannot be run using Rscript. I have tried using the script from v0.3.2.

[ycl6]

Hi @sroener

With ichorCNA v0.5, the analysis need to be performed inside R using the run_ichorCNA function. Below is an example that I adapted from that you provided.

Also, you'll need to get a copy of the repTime wig from inst/extdata, e.g. Koren_repTiming_hg38_1000kb.wig that I used in the example.

ichorCNA::run_ichorCNA(id = "test19_processed", 
  tumor_wig = "results/testrun/icorCNA/readcounts/test19_index_processed.hg19.wig",
  gcWig = "resources/ichorCNA/gc_hg19_1000kb.wig", 
  mapWig = "resources/ichorCNA/map_hg19_1000kb.wig", 
  repTimeWig = "Koren_repTiming_hg38_1000kb.wig", # Get it from "inst/extdata"
  normal_panel = "resources/ichorCNA/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds",
  centromere = "resources/ichorCNA/GRCh37.p13_centromere_UCSC-gapTable.txt",
  ploidy = "c(2,3)",
  normal = "c(0.5,0.6,0.7,0.8,0.9)",
  maxCN = 5,
  scStates = "c(1,3)",
  chrs = 'c(1:22,"X")',		# default
  chrTrain = "c(1:22)",		# default
  estimateNormal = TRUE,	# default
  estimatePloidy = TRUE,	# default
  estimateScPrevalence = TRUE,	# default
  includeHOMD = FALSE,		# default
  txnE = 0.9999,
  txnStrength = 10000,
  plotFileType = "png",
  genomeBuild = "hg19",
  genomeStyle = "UCSC",
  outDir = "results/testrun/icorCNA/test19_processed_hg19", # Folder need to exist
)

[sroener]

Hi @ycl6

thank you for your answer.

Could you provide a little background on what Koren_repTiming_hg38_1000kb.wig does?

In the past I used ichorCNA in a pipeline using the runIchorCNA.r CLI in a rule for processing a huge amount of samples. As I think that providing CLIs and functional interfaces for end-to-end tools, I am wondering whether there is a particular reason for dropping the CLI?

[ycl6]

Hi @sroener

repTiming takes a wig file that has replication timing data. Amnon Koren is a leading researcher of this field and you can see a figure on his website that illustrate how replication timing influences copy number along a chromosome during DNA replication. Like other CNA tools, correction for replication timing can be enabled to better profile CNV events. Ideally, you will/can use the replication timing data from your cell/tissue type (assayed using Repli-seq or inferred from WGS) to perform correction. Though, replication timing is highly conserved, you can try publicly available resources, such as that provided here. @gavinha can probably share where the replication timing tracks were sourced and how they were converted into wig files.

The repTimeWig param should be an optional input but a bug with the current version means you do need to supply one. You can try PR #15 and that should allow you to run ichorCNA without replication timing wig.

@gavinha can probably explain why the CLI version is dropped (or not have a script to work alongside the current run_ichorCNA function). It is not too difficult to write one to work with the current version. I can chip in if the maintainer does not already have one.

[lbeltrame]

It would be very useful to have a working CLI. Otherwise, to work in containers during workflows (e.g. in nextflow, snakemake, WDL, you name it), everyone would need to reinvent the wheel.

[xiucz]

Hi, @ycl6
Do you know how to create a repTimeWig file? I need a 50kb binsize file for hg19, but I have found very limited information online.

Best,
xiucz

[ycl6]

Hi @xiucz

You might want to contact @gavinha and ask how he creates the repTimeWig files provided in this repo.

One of the repTimeWig files is in 50kb binsize: Koren_repTiming_hg19_50kb.wig

https://github.com/GavinHaLab/ichorCNA/tree/master/inst/extdata