Hello there,
I am just started playing with ChIPQC and DiffBind but I am failing miserably at just loading the sample data. I have downloaded the DiffBind Package data from your website (https://www.dropbox.com/s/gfc49wul2bv5nz6/DiffBind_vignette_data.tar.gz)
My script looks like:
# load libraries library(ChIPQC) library(DiffBind) # read in files samples = read.csv(file="chipqc_trial/DiffBind_Vignette/tamoxifen.csv") exampleExp = ChIPQC(samples) exampleDB = dba(sampleSheet="chipqc_trial/DiffBind_Vignette/tamoxifen.csv")
When I run:
> exampleExp = ChIPQC(samples)
I get:
BT4741 BT474 ER Resistant Full-Media 1 bed
Error in if (file.info(peaks)$size > 0) { :
missing value where TRUE/FALSE needed
> traceback()
4: pv.peakset(model, peaks = as.character(samples$Peaks[i]), sampID = as.character(samples$SampleID[i]),
tissue = as.character(samples$Tissue[i]), factor = as.character(samples$Factor[i]),
condition = as.character(samples$Condition[i]), treatment = as.character(samples$Treatment[i]),
consensus = F, peak.caller = peakcaller, peak.format = peakformat,
scoreCol = peakscores, bLowerScoreBetter = peaksLowerBetter,
control = controlid, reads = NA, replicate = as.integer(samples$Replicate[i]),
readBam = as.character(samples$bamReads[i]), controlBam = as.character(samples$bamControl[i]),
filter = peakfilter, counts = counts, bRemoveM = bRemoveM,
bRemoveRandom = bRemoveRandom, skipLines = skipLines)
3: pv.model(DBA, mask = mask, minOverlap = minOverlap, samplesheet = sampleSheet,
config = config, caller = peakCaller, format = peakFormat,
scorecol = scoreCol, bLowerBetter = bLowerScoreBetter, skipLines = skipLines,
bAddCallerConsensus = bAddCallerConsensus, bRemoveM = bRemoveM,
bRemoveRandom = bRemoveRandom, filter = filter, attributes = attributes,
dir)
2: dba(sampleSheet = experiment, bCorPlot = FALSE, peakCaller = "bed")
1: ChIPQC(samples)
___
I have tried a number of different things, I tried using my own files (which are macs2 peaks and bowtie2 bam files).
Any ideas of what can be going on? Is this a version incompatibility?
Many thanks!
Anna
> sessionInfo() R version 3.5.0 (2018-04-23) 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_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPQC_1.16.0 DiffBind_2.8.0 SummarizedExperiment_1.10.1 DelayedArray_0.6.5 [5] BiocParallel_1.14.2 matrixStats_0.54.0 Biobase_2.40.0 GenomicRanges_1.32.6 [9] GenomeInfoDb_1.16.0 IRanges_2.14.10 S4Vectors_0.18.3 BiocGenerics_0.26.0 [13] ggplot2_3.0.0 BiocInstaller_1.30.0 loaded via a namespace (and not attached): [1] amap_0.8-16 colorspace_1.3-2 [3] rjson_0.2.20 hwriter_1.3.2 [5] XVector_0.20.0 base64enc_0.1-3 [7] rstudioapi_0.7 ggrepel_0.8.0 [9] bit64_0.9-7 AnnotationDbi_1.42.1 [11] splines_3.5.0 TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 [13] Nozzle.R1_1.1-1 Rsamtools_1.32.2 [15] annotate_1.58.0 GO.db_3.6.0 [17] pheatmap_1.0.10 graph_1.58.0 [19] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2 compiler_3.5.0 [21] httr_1.3.1 GOstats_2.46.0 [23] backports_1.1.2 assertthat_0.2.0 [25] Matrix_1.2-14 lazyeval_0.2.1 [27] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 limma_3.36.2 [29] prettyunits_1.0.2 tools_3.5.0 [31] bindrcpp_0.2.2 gtable_0.2.0 [33] glue_1.3.0 GenomeInfoDbData_1.1.0 [35] Category_2.46.0 reshape2_1.4.3 [37] systemPipeR_1.14.0 dplyr_0.7.6 [39] ShortRead_1.38.0 Rcpp_0.12.18 [41] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 [43] Biostrings_2.48.0 gdata_2.18.0 [45] rtracklayer_1.40.4 TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 [47] stringr_1.3.1 gtools_3.8.1 [49] XML_3.98-1.15 edgeR_3.22.3 [51] zlibbioc_1.26.0 scales_1.0.0 [53] hms_0.4.2 RBGL_1.56.0 [55] RColorBrewer_1.1-2 BBmisc_1.11 [57] yaml_2.2.0 memoise_1.1.0 [59] biomaRt_2.36.1 latticeExtra_0.6-28 [61] stringi_1.2.4 RSQLite_2.1.1 [63] genefilter_1.62.0 checkmate_1.8.5 [65] GenomicFeatures_1.32.2 caTools_1.17.1.1 [67] chipseq_1.30.0 rlang_0.2.1 [69] pkgconfig_2.0.2 BatchJobs_1.7 [71] bitops_1.0-6 TxDb.Celegans.UCSC.ce6.ensGene_3.2.2 [73] lattice_0.20-35 purrr_0.2.5 [75] bindr_0.1.1 GenomicAlignments_1.16.0 [77] bit_1.1-14 tidyselect_0.2.4 [79] GSEABase_1.42.0 AnnotationForge_1.22.2 [81] plyr_1.8.4 magrittr_1.5 [83] sendmailR_1.2-1 R6_2.2.2 [85] gplots_3.0.1 DBI_1.0.0 [87] pillar_1.3.0 withr_2.1.2 [89] survival_2.42-6 RCurl_1.95-4.11 [91] tibble_1.4.2 crayon_1.3.4 [93] KernSmooth_2.23-15 progress_1.2.0 [95] locfit_1.5-9.1 grid_3.5.0 [97] data.table_1.11.4 blob_1.1.1 [99] Rgraphviz_2.24.0 digest_0.6.15 [101] xtable_1.8-2 brew_1.0-6 [103] munsell_0.5.0
I guess this is solved for problem in example and can be closed
Hi Tom,
Thank you for getting back to me. The error persists.
The files are in the correct directory (note that read.csv() ) does not fail).
In addtion, the DBA example also fails:
> exampleDB = dba(sampleSheet="DiffBind_Vignette/tamoxifen.csv")
BT4741 BT474 ER Resistant Full-Media 1 bed
Error in if file.info(peaks)$size > 0) { :
missing value where TRUE/FALSE needed
I have also picked up another error message when running the project from scratch from the same directory. I am not sure if this is related?
Error: package or namespace load failed for ‘ChIPQC’:
.onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
call: initialize(value, ...)
error: attempt to apply non-function
Error in .requirePackage(package) :
unable to find required package ‘ChIPQC’
In addition: Warning messages:
1: package ‘GenomicRanges’ was built under R version 3.5.1
2: package ‘DelayedArray’ was built under R version 3.5.1
Loading required package: ChIPQC
Error: package or namespace load failed for ‘ChIPQC’:
.onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
call: .Object$initialize(...)
error: attempt to apply non-function
Error in .requirePackage(package) :
unable to find required package ‘ChIPQC’
In addition: Warning message:
call dbDisconnect() when finished working with a connection
hi Anna,
As the Dffbind command is not working this suggest the wrong working directory.
The CSV you are reading lists files as relative paths from the location inside the Diffbind vignette directory. So reading the CSV will work but it will not be able to find any files unless you are in same directory as CSV.
The bamReads column lists files in a directory called "reads/" for instance.
> samples = read.csv(file="tamoxifen.csv")
> samples$bamReads
> samples$bamReads
[1] reads/Chr18_BT474_ER_1.bam reads/Chr18_BT474_ER_2.bam reads/Chr18_MCF7_ER_1.bam reads/Chr18_MCF7_ER_2.bam reads/Chr18_MCF7_ER_3.bam
[6] reads/Chr18_T47D_ER_1.bam reads/Chr18_T47D_ER_2.bam reads/Chr18_TAMR_ER_1.bam reads/Chr18_TAMR_ER_2.bam reads/Chr18_ZR75_ER_1.bam
[11] reads/Chr18_ZR75_ER_2.bam
11 Levels: reads/Chr18_BT474_ER_1.bam reads/Chr18_BT474_ER_2.bam reads/Chr18_MCF7_ER_1.bam reads/Chr18_MCF7_ER_2.bam ... reads/Chr18_ZR75_ER_2.bam
The other message looks unrelated to this problem,
vb,
tom
hi Anna,
Did you try moving to DiffBind_Vignette directory?
tom
Thanks Tom. It is working now.
hi Anna,
Do you mind accepting my answer at the top?
thank you,
tom