Question: ATAC-Seq peaks quality control with ChIPQC package, but getting error
0
gravatar for Subinoy Biswas
9 months ago by
Subinoy Biswas10 wrote:

I am doing a quality check of my ATAC-Seq peaks with ChIPQC package but I am getting an error.

Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL",  : 
  'names' attribute [9] must be the same length as the vector [7]

So, I need help to solve the issue. Below is my sample sheet.

> sampleid  Tissue  Factor  Condition   Treatment   Replicate   bamReads    ControlID   bamControl  Peaks   PeakCaller

> BD24  Tumor       Eight   2018    1   bam_reads/BD24_bam.bam  BD03    bam_reads/BD03_bam.bam  peaks_BD03_ref_data/q_05/BD24_peaks.narrowPeak  macs

> BD28  Tumor       Eight   2018    2   bam_reads/BD28_bam.bam  BD031   bam_reads/BD03_bam.bam  peaks_BD03_ref_data/q_05/BD28_peaks.narrowPeak  macs

> BD07  Tumor       Twelve  2016    1   bam_reads/BD07_bam.bam  BD032   bam_reads/BD03_bam.bam  peaks_BD03_ref_data/q_05/BD07_peaks.narrowPeak  macs

> BD11  Tumor       Twelve  2017    2   bam_reads/BD11_bam.bam  BD033   bam_reads/BD03_bam.bam  peaks_BD03_ref_data/q_05/BD11_peaks.narrowPeak  macs

Here is my code

    library(DiffBind)
    library(ChIPseeker)
    library(org.Mm.eg.db)
    library(bedr)
    library(ChIPQC)
    library(BiocParallel)
    register(SerialParam())
    samples <- read.csv("cd4_meta_8_12_BD03_q_05_test.csv", header = T)
    proj1 = ChIPQC(samples,annotation = 'mm10',chromosomes = "chrY")
    proj1

proj1 = ChIPQC(samples,annotation = 'mm10',chromosomes = "chrY")

1 Tumor  Eight 2018 1 macs


2 Tumor  Eight 2018 2 macs

3 Tumor  Twelve 2016 1 macs

4 Tumor  Twelve 2017 2 macs

Compiling annotation...
Computing metrics for 5 samples...
list
Bam file has 138 contigs
Calculating coverage histogram for chrY

Calculating SSD for chrY

Calculating unique positions per strand for chrY

Calculating shift for chrY

 300 / 300
Counting reads in features for chrY

Signal over peaks for chrY

done
Calculating coverage
Calculating Summits on  chrY  ..[1] 1
list
Bam file has 138 contigs
Calculating coverage histogram for chrY

Calculating SSD for chrY

Calculating unique positions per strand for chrY

Calculating shift for chrY

 300 / 300
Counting reads in features for chrY

Signal over peaks for chrY

done
Calculating coverage
Calculating Summits on  chrY  ..[1] 1
list
Bam file has 138 contigs
Calculating coverage histogram for chrY

Calculating SSD for chrY

Calculating unique positions per strand for chrY

Calculating shift for chrY

 300 / 300
Counting reads in features for chrY

Signal over peaks for chrY

done
Calculating coverage
Calculating Summits on  chrY  ..[1] 1
list
Bam file has 138 contigs
Calculating coverage histogram for chrY

Calculating SSD for chrY

Calculating unique positions per strand for chrY

Calculating shift for chrY

 300 / 300
Counting reads in features for chrY

Signal over peaks for chrY

done
Calculating coverage
Calculating Summits on  chrY  ..[1] 1
list
Bam file has 138 contigs
Calculating coverage histogram for chrY

Calculating SSD for chrY

Calculating unique positions per strand for chrY

Calculating shift for chrY

 300 / 300
Counting reads in features for chrY

[1] 1
**Warning messages:**

1: In if is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used

2: In if is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used

3: In if is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used

4: In if is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used

 **proj1**

> Samples: 5 : 1 2 3 4 BD03 

>  Tissue Condition Treatment Control Replicate Peaks

> 1  Tumor     Eight      2018    BD03         1 14156

> 2  Tumor     Eight      2018   BD031         2  4052

> 3  Tumor    Twelve      2016   BD032         1  3968

> 4  Tumor    Twelve      2017   BD033         2 14339




**Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL",  : 
  'names' attribute [9] must be the same length as the vector [7]**
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] org.Mm.eg.db_3.7.0          AnnotationDbi_1.44.0        ChIPQC_1.18.0               ggplot2_3.1.0              
 [5] bindrcpp_0.2.2              bedr_1.0.6                  ChIPseeker_1.18.0           TCseq_1.6.0                
 [9] rmarkdown_1.11              DiffBind_2.10.0             SummarizedExperiment_1.12.0 DelayedArray_0.8.0         
[13] BiocParallel_1.16.2         matrixStats_0.54.0          Biobase_2.42.0              GenomicRanges_1.34.0       
[17] GenomeInfoDb_1.18.1         IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
  [1] R.utils_2.7.0                             tidyselect_0.2.5                         
  [3] RSQLite_2.1.1                             htmlwidgets_1.3                          
  [5] grid_3.5.1                                BatchJobs_1.7                            
  [7] munsell_0.5.0                             units_0.6-2                              
  [9] systemPipeR_1.16.0                        withr_2.1.2                              
 [11] colorspace_1.4-0                          GOSemSim_2.8.0                           
 [13] Category_2.48.0                           knitr_1.21                               
 [15] rstudioapi_0.9.0                          DOSE_3.8.0                               
 [17] labeling_0.3                              urltools_1.7.1                           
 [19] GenomeInfoDbData_1.2.0                    hwriter_1.3.2                            
 [21] bit64_0.9-7                               farver_1.1.0                             
 [23] pheatmap_1.0.12                           TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
 [25] lambda.r_1.2.3                            xfun_0.4                                 
 [27] R6_2.3.0                                  locfit_1.5-9.1                           
 [29] bitops_1.0-6                              fgsea_1.8.0                              
 [31] gridGraphics_0.3-0                        assertthat_0.2.0                         
 [33] scales_1.0.0                              ggraph_1.0.2                             
 [35] nnet_7.3-12                               enrichplot_1.2.0                         
 [37] gtable_0.2.0                              rlang_0.3.1                              
 [39] genefilter_1.64.0                         BBmisc_1.11                              
 [41] splines_3.5.1                             rtracklayer_1.42.1                       
 [43] lazyeval_0.2.1                            acepack_1.4.1                            
 [45] europepmc_0.3                             brew_1.0-6                               
 [47] checkmate_1.9.0                           yaml_2.2.0                               
 [49] reshape2_1.4.3                            TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
 [51] GenomicFeatures_1.34.1                    backports_1.1.3                          
 [53] qvalue_2.14.0                             Hmisc_4.1-1                              
 [55] RBGL_1.58.1                               tools_3.5.1                              
 [57] ggplotify_0.0.3                           gridBase_0.4-7                           
 [59] gplots_3.0.1                              RColorBrewer_1.1-2                       
 [61] ggridges_0.5.1                            Rcpp_1.0.0                               
 [63] plyr_1.8.4                                base64enc_0.1-3                          
 [65] progress_1.2.0                            zlibbioc_1.28.0                          
 [67] purrr_0.2.5                               RCurl_1.95-4.11                          
 [69] prettyunits_1.0.2                         rpart_4.1-13                             
 [71] viridis_0.5.1                             cowplot_0.9.4                            
 [73] chipseq_1.32.0                            ggrepel_0.8.0                            
 [75] cluster_2.0.7-1                           magrittr_1.5                             
 [77] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2   data.table_1.12.0                        
 [79] futile.options_1.0.1                      DO.db_2.9                                
 [81] triebeard_0.3.0                           amap_0.8-16                              
 [83] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2   hms_0.4.2                                
 [85] evaluate_0.12                             xtable_1.8-3                             
 [87] XML_3.98-1.16                             VennDiagram_1.6.20                       
 [89] gridExtra_2.3                             testthat_2.0.1                           
 [91] compiler_3.5.1                            biomaRt_2.38.0                           
 [93] tibble_2.0.1                              KernSmooth_2.23-15                       
 [95] crayon_1.3.4                              R.oo_1.22.0                              
 [97] htmltools_0.3.6                           GOstats_2.48.0                           
 [99] Formula_1.2-3                             geneplotter_1.60.0                       
[101] sendmailR_1.2-1                           DBI_1.0.0                                
[103] tweenr_1.0.1                              formatR_1.5                              
[105] MASS_7.3-51.1                             boot_1.3-20                              
[107] ShortRead_1.40.0                          Matrix_1.2-15                            
[109] R.methodsS3_1.7.1                         gdata_2.18.0                             
[111] bindr_0.1.1                               igraph_1.2.2                             
[113] pkgconfig_2.0.2                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
[115] rvcheck_0.1.3                             GenomicAlignments_1.18.0                 
[117] foreign_0.8-71                            TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
[119] xml2_1.2.0                                annotate_1.60.0                          
[121] XVector_0.22.0                            AnnotationForge_1.24.0                   
[123] stringr_1.3.1                             digest_0.6.18                            
[125] graph_1.60.0                              Biostrings_2.50.1                        
[127] fastmatch_1.1-0                           htmlTable_1.13.1                         
[129] edgeR_3.24.2                              GSEABase_1.44.0                          
[131] Rsamtools_1.34.0                          gtools_3.8.1                             
[133] rjson_0.2.20                              jsonlite_1.6                             
[135] futile.logger_1.4.3                       viridisLite_0.3.0                        
[137] limma_3.38.3                              pillar_1.3.1                             
[139] Nozzle.R1_1.1-1                           lattice_0.20-38                          
[141] httr_1.4.0                                plotrix_3.7-4                            
[143] survival_2.43-3                           GO.db_3.7.0                              
[145] glue_1.3.0                                UpSetR_1.3.3                             
[147] bit_1.1-14                                Rgraphviz_2.26.0                         
[149] ggforce_0.1.3                             class_7.3-15                             
[151] stringi_1.2.4                             blob_1.1.1                               
[153] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4  DESeq2_1.22.1                            
[155] latticeExtra_0.6-28                       caTools_1.17.1.1                         
[157] memoise_1.1.0                             dplyr_0.7.8                              
[159] e1071_1.7-0
--------------------

Please suggest me how to solve this error.

Thanks, SB

chipqc atac-seq • 392 views
ADD COMMENTlink modified 9 months ago by James W. MacDonald51k • written 9 months ago by Subinoy Biswas10

Thanks, @James W. MacDonald for properly formatting the query.

ADD REPLYlink written 9 months ago by Subinoy Biswas10

Got the same error. Is there any update?

ADD REPLYlink written 5 months ago by analeigh.gui10

Got the same error. Any resolution?

ADD REPLYlink written 3 months ago by zhenfeng.liu110

The problem is caused by single end data which would not return fragment length. I fixed it in my fork project. And I contacted the author and hope they will fix it in their next release.

https://github.com/shengqh/ChIPQC

ADD REPLYlink written 9 weeks ago by shengqh0
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