Entering edit mode
ChIPQCreport requires that the "Replicate" of each sample be provided during the construction of its experiment object.
If it is not provided, ChIPQCreport fails with a cryptic error, even if invoked for only a single experimental sample:
> samples
SampleID Tissue Factor bamReads ControlID
1 ENCFF863PSQ DOHH2 CTCF ENCFF863PSQ.sorted.markeddup.bam ENCFF631ENA
bamControl Peaks
1 ENCFF631ENA.sorted.markeddup.bam NA
> experiment <- ChIPQC(samples, annotation="hg38")
> ChIPQCreport(experiment, F)
Saving 7 x 7 in image
Error in seq.default(h[1], h[2], length.out = n) :
'to' cannot be NA, NaN or infinite
> traceback()
25: stop("'to' cannot be NA, NaN or infinite")
24: seq.default(h[1], h[2], length.out = n)
23: seq(h[1], h[2], length.out = n)
22: rotate(seq(h[1], h[2], length.out = n))
21: f(...)
20: self$palette(n)
19: f(..., self = self)
18: self$map(df[[j]])
17: FUN(X[[i]], ...)
16: lapply(aesthetics, function(j) self$map(df[[j]]))
15: f(..., self = self)
14: scale$map_df(df = df)
13: FUN(X[[i]], ...)
12: lapply(scales$scales, function(scale) scale$map_df(df = df))
11: unlist(lapply(scales$scales, function(scale) scale$map_df(df = df)),
recursive = FALSE)
10: FUN(X[[i]], ...)
9: lapply(data, scales_map_df, scales = npscales)
8: ggplot_build(x)
7: print.ggplot(x)
6: print(x)
5: grid.draw.ggplot(plot)
4: grid.draw(plot)
3: ggsave(plotCC(object, facet = facet, facetBy = facetBy, colourBy = colourBy,
lineBy = lineBy, addMetaData = addMetaData), filename = file.path(reportFolder,
"CCPlot.png"))
2: ChIPQCreport(experiment, F)
1: ChIPQCreport(experiment, F)
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ChIPQC_1.8.7 DiffBind_2.0.2
[3] SummarizedExperiment_1.2.3 Biobase_2.32.0
[5] GenomicRanges_1.24.2 GenomeInfoDb_1.8.1
[7] IRanges_2.6.1 S4Vectors_0.10.1
[9] BiocGenerics_0.18.0 ggplot2_2.1.0
loaded via a namespace (and not attached):
[1] edgeR_3.14.0
[2] splines_3.3.0
[3] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
[4] TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2
[5] gtools_3.5.0
[6] assertthat_0.1
[7] latticeExtra_0.6-28
[8] amap_0.8-14
[9] RBGL_1.48.1
[10] Rsamtools_1.24.0
[11] Category_2.38.0
[12] RSQLite_1.0.0
[13] backports_1.0.2
[14] lattice_0.20-33
[15] limma_3.28.10
[16] digest_0.6.10
[17] RColorBrewer_1.1-2
[18] XVector_0.12.0
[19] checkmate_1.8.0
[20] colorspace_1.2-6
[21] Matrix_1.2-6
[22] plyr_1.8.4
[23] GSEABase_1.34.0
[24] chipseq_1.22.0
[25] TxDb.Hsapiens.UCSC.hg38.knownGene_3.1.3
[26] XML_3.98-1.4
[27] pheatmap_1.0.8
[28] ShortRead_1.30.0
[29] biomaRt_2.28.0
[30] genefilter_1.54.2
[31] zlibbioc_1.18.0
[32] xtable_1.8-2
[33] GO.db_3.3.0
[34] scales_0.4.0
[35] brew_1.0-6
[36] gdata_2.17.0
[37] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2
[38] BiocParallel_1.6.2
[39] annotate_1.50.0
[40] GenomicFeatures_1.24.2
[41] survival_2.39-4
[42] magrittr_1.5
[43] systemPipeR_1.6.2
[44] fail_1.3
[45] gplots_3.0.1
[46] hwriter_1.3.2
[47] GOstats_2.38.0
[48] graph_1.50.0
[49] tools_3.3.0
[50] BBmisc_1.9
[51] stringr_1.1.0
[52] sendmailR_1.2-1
[53] munsell_0.4.3
[54] locfit_1.5-9.1
[55] AnnotationDbi_1.34.3
[56] Biostrings_2.40.2
[57] caTools_1.17.1
[58] grid_3.3.0
[59] RCurl_1.95-4.8
[60] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2
[61] rjson_0.2.15
[62] AnnotationForge_1.14.2
[63] bitops_1.0-6
[64] base64enc_0.1-3
[65] gtable_0.2.0
[66] DBI_0.4-1
[67] reshape2_1.4.1
[68] R6_2.1.3
[69] GenomicAlignments_1.8.3
[70] Nozzle.R1_1.1-1
[71] dplyr_0.4.3
[72] rtracklayer_1.32.1
[73] KernSmooth_2.23-15
[74] stringi_1.1.1
[75] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[76] BatchJobs_1.6
[77] Rcpp_0.12.7
[78] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[79] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
This error does not occur for an identical invocation of ChIPQCreport for an experiment object whose sample was assigned "Replicate" = 1.
Great, thanks Rory.
Thanks, Rory!
Might it be possible to add a check for that within
ChIPQCreportitself (and for it to automatically use theChIPQCsampleobject, from theChIPQCexperiment), to prevent users from needing to use a workaround with only a single sample (i.e. to maintain a consistent API)?The ChIPQCreport() function should generate reports from ChIPQCexperiment and ChIPQCsample in a very similar manner.
In your case the below examples would give equivalent results. This would work with Replicates are NA as in your case.
> ChIPQCreport(QCsample(experiment)[[1]])
> ChIPQCreport(experiment,facetBy="Sample",colourBy=NULL,lineBy=NULL)
Both ChIPQCsample and ChIPQCexperiment reports should contain the same information but when creating from an ChIPQCexperiment, various aesthetics are filled in from the samplesheet or user defined metadata. By default we use Replicate to colour lines and so in your case this failed. One immediate solution, as Rory recommends, is to simply work with one sample and no metadata - first example, the other immediate solution is to set parameters such as "facetBy","Sample","lineBy","colourBy" to columns with metadata.
I agree a check for valid columns is required and will look to implement in the future.
best,
tom
I appreciate this useful information!
I will keep that workaround in mind and am glad to hear that.
Thanks,
Coby
Just wanted to follow-up on this. This workaround is still needed in the latest version (1.12.0) and the same cryptic error message is emitted without it.