How to use panelcn.mops to detect CNVs from whole genome data by getting count windows from BED file?
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@metzgerlukas-23050
Last seen 14 months ago

Hi, I am using panelcn.mops to detect CNVs from whole genome data by comparing cases vs controls. I have several controls and want to compare them to one sample. For this, I am using the Agilent V6 bed file, which I downloaded from SureDesigns. For my purpose I would like to get the CNVs from the whole genome data, not only from a specific gene region.

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_DE.UTF-8   
 [6] LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] panelcn.mops_1.8.0   cn.mops_1.32.0       GenomicRanges_1.38.0 GenomeInfoDb_1.22.0  IRanges_2.20.2       S4Vectors_0.24.3    
[7] BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] Biostrings_2.54.0      Rsamtools_2.2.3        bitops_1.0-6           exomeCopy_1.32.0       zlibbioc_1.32.0        XVector_0.26.0        
 [7] BiocParallel_1.20.1    tools_3.6.1            Biobase_2.46.0         RCurl_1.98-1.1         compiler_3.6.1         BiocManager_1.30.10   
[13] GenomeInfoDbData_1.2.2

My code looks like this:

#

bedfile <- "Agilent/S07604624_Regions.bed"
countWindow <- getWindows(bedfile)

BAMFiles_m <- list.files("Controls", pattern=".bam$", full.names=TRUE)
test_sample <- "test_sample.bam"
controls<- countBamListInGRanges(countWindows = countWindows, bam.files  = BAMFiles_m, read.width=150)
cases<-countBamListInGRanges(countWindows = countWindows,bam.files  = test_sample, read.width=150)
elementMetadata(cases) <- cbind(elementMetadata(cases), elementMetadata(controls))

resultlist<- runPanelcnMops(cases, countWindows=countWindow)
#

When running the "runPanelcnMops" command it starts with the first few windows, but then I get an error:

Analyzing sample(s) test_sample.bam
new sampleThresh 71.5

Had to reduce read counts for exon HRNR.NM_001009931.ens|ENST00000420707.ens|ENST00000593011.ens|ENST00000368801.ccds|CCDS30859
Had to reduce read counts for exon MUC4.NM_018406.NM_001322468.NM_138297.NM_004532.ens|ENST00000349607.ens|ENST00000346145.ens|ENST00000478156.ens|ENST00000466475.ens|ENST00000477756.ens|ENST00000475231.ens|ENST00000479406.ens|ENST00000470451.ens|ENST00000480843.ens|ENST00000462323.ens|ENST00000477086.ens|ENST00000463781.ccds|CCDS54700.ccds|CCDS3311.ccds|CCDS3310
Had to reduce read counts for exon MUC4.NM_018406.NM_001322468.NM_138297.NM_004532.ens|ENST00000349607.ens|ENST00000346145.ens|ENST00000478156.ens|ENST00000466475.ens|ENST00000477756.ens|ENST00000475231.ens|ENST00000479406.ens|ENST00000470451.ens|ENST00000480843.ens|ENST00000462323.ens|ENST00000477086.ens|ENST00000463781.ccds|CCDS54700.ccds|CCDS3311.ccds|CCDS3310
Had to reduce read counts for exon MUC4.NM_018406.NM_001322468.NM_138297.NM_004532.ens|ENST00000349607.ens|ENST00000346145.ens|ENST00000478156.ens|ENST00000466475.ens|ENST00000477756.ens|ENST00000475231.ens|ENST00000479406.ens|ENST00000470451.ens|ENST00000480843.ens|ENST00000462323.ens|ENST00000477086.ens|ENST00000463781.ccds|CCDS54700.ccds|CCDS3311.ccds|CCDS3310
Had to reduce read counts for exon -

Error: C stack usage  7969597 is too close to the limit

Do you know what is the problem? Or am I using the wrong code for this purpose?

cn.mops panelcn.mops CNV detection CNV • 87 views
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