Hello!
After importing a wig file and liftover from mm9 to mm10 and unlisting to get a GRanges object, I encounter an error where the seqinfo data is not included in the Granges file such that I can't export a bigWig file using export.bw.
wig <- import.wig("GSM1463433_ProB_H3K27ac.wig")
chain <- import.chain("mm9ToMm10.over.chain")
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
wig_mm10 <- liftOver(wig, chain)
wig_mm10.unlist <- unlist(wig_mm10)
export.bw(wig_mm10.unlist, con="GSM1463433_ProB_H3K27ac.wig_mm10.bigWig")
A previous developer solution was to specify the genome in export.bw eg. export.bw(obj, con="", genome=""), however, genome isn't recognised as a function in export.bw
> seqinfo(wig_mm10.unlist)
Seqinfo object with 22 sequences from an unspecified genome; no seqlengths:
seqnames seqlengths isCircular genome
chr1 <NA> <NA> <NA>
chr12 <NA> <NA> <NA>
chr2 <NA> <NA> <NA>
chr15 <NA> <NA> <NA>
chr3 <NA> <NA> <NA>
... ... ... ...
chr19 <NA> <NA> <NA>
chr13 <NA> <NA> <NA>
chrY <NA> <NA> <NA>
chr18 <NA> <NA> <NA>
chrM <NA> <NA> <NA>
When I have manually entered in seqinfo, I still can get an error where there are overlapping ranges within the GRanges object such that I can't export to a bigWig file even with the seqInfo.
Would someone be able to shed some light on this?
Cheers
A
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
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_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] diffloop_1.8.0 BiocInstaller_1.30.0
[3] knitr_1.20 AnnotationHub_2.12.1
[5] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[7] GenomicFeatures_1.32.3 rtracklayer_1.40.6
[9] GenomicAlignments_1.16.0 SummarizedExperiment_1.10.1
[11] DelayedArray_0.6.6 BiocParallel_1.14.2
[13] matrixStats_0.54.0 Rsamtools_1.32.3
[15] Biostrings_2.48.0 XVector_0.20.0
[17] GenomicRanges_1.32.7 GenomeInfoDb_1.16.0
[19] ggplot2_3.1.0 EGSEA_1.8.0
[21] pathview_1.20.0 org.Hs.eg.db_3.6.0
[23] topGO_2.32.0 SparseM_1.77
[25] GO.db_3.6.0 graph_1.58.2
[27] AnnotationDbi_1.42.1 IRanges_2.14.12
[29] S4Vectors_0.18.3 gage_2.30.0
[31] Biobase_2.40.0 BiocGenerics_0.26.0
[33] limma_3.36.5
