Question: ATAC-QC shiftGAlignmentsList function
0
Shuang He • 0 wrote:
I tried to use ATAC-QC to generate the ATAC-seq QC plots , but I met some problem with the shiftGAlignmentsList function. Thank you for your help in advance.
bamfile <- "G:/project/ATAC-seq_QC/rdrmbam/my.rdrm.bam"
possibleTag <- combn(LETTERS, 2)
possibleTag <- c(paste0(possibleTag[1, ], possibleTag[2, ]),
paste0(possibleTag[2, ], possibleTag[1, ]))
library(Rsamtools)
bamTop100 <- scanBam(BamFile(bamfilde, yieldSize = 100),
param = ScanBamParam(tag=possibleTag))[[1]]$tag
tags <- names(bamTop100)[lengths(bamTop100)>0]
> tags
[1] "AS" "MD" "XG" "NM" "XM" "XN" "XO" "XS" "YS" "YT"
library(BSgenome.Mmusculus.UCSC.mm10)
seqlev <- "chr1" ## subsample data for quick run
which <- as(seqinfo(Mmusculus)[seqlev], "GRanges")
> which
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
chr1 chr1 1-195471971 *
seqinfo: 1 sequence from mm10 genome
mygal <- readBamFile(bamfile, tag=tags, which=which, asMates= TRUE, bigFile=TRUE)
>mygal
GAlignmentsList object of length 0:
<0 elements>
seqinfo: no sequences
mygal1 <- shiftGAlignmentsList(mygal#,
+ #outbam=shiftedBamfile
+ )
>Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'readGAlignments' for signature '"NULL"'
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.34.8
[3] AnnotationDbi_1.44.0 BSgenome.Hsapiens.UCSC.hg19_1.4.0
[5] BSgenome.Mmusculus.UCSC.mm10_1.4.0 BSgenome_1.50.0
[7] rtracklayer_1.42.0 RColorBrewer_1.1-2
[9] ATACseqQC_1.6.4 GenomicAlignments_1.18.1
[11] Rsamtools_1.34.0 Biostrings_2.50.1
[13] XVector_0.22.0 SummarizedExperiment_1.12.0
[15] DelayedArray_0.8.0 BiocParallel_1.16.0
[17] matrixStats_0.54.0 Biobase_2.42.0
[19] GenomicRanges_1.34.0 GenomeInfoDb_1.18.0
[21] IRanges_2.16.0 S4Vectors_0.20.0
[23] BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.14.0 bitops_1.0-6 bit64_0.9-7
[4] progress_1.2.0 httr_1.3.1 tools_3.5.1
[7] R6_2.3.0 rGADEM_2.30.0 KernSmooth_2.23-15
[10] seqLogo_1.48.0 DBI_1.0.0 lazyeval_0.2.1
[13] colorspace_1.3-2 ade4_1.7-13 motifStack_1.26.0
[16] prettyunits_1.0.2 bit_1.1-14 curl_3.2
[19] compiler_3.5.1 VennDiagram_1.6.20 graph_1.60.0
[22] formatR_1.5 grImport_0.9-2 scales_1.0.0
[25] randomForest_4.6-14 RBGL_1.58.0 stringr_1.3.1
[28] digest_0.6.18 pkgconfig_2.0.2 htmltools_0.3.6
[31] ensembldb_2.6.8 limma_3.38.2 regioneR_1.14.0
[34] htmlwidgets_1.3 rlang_0.3.0.1 rstudioapi_0.8
[37] RSQLite_2.1.1 shiny_1.2.0 RCurl_1.95-4.11
[40] magrittr_1.5 polynom_1.3-9 GO.db_3.7.0
[43] GenomeInfoDbData_1.2.0 futile.logger_1.4.3 Matrix_1.2-14
[46] Rcpp_1.0.0 munsell_0.5.0 stringi_1.2.4
[49] yaml_2.2.0 MASS_7.3-50 zlibbioc_1.28.0
[52] AnnotationHub_2.14.1 grid_3.5.1 blob_1.1.1
[55] promises_1.0.1 crayon_1.3.4 lattice_0.20-35
[58] splines_3.5.1 multtest_2.38.0 hms_0.4.2
[61] GenomicScores_1.6.0 MotIV_1.38.0 seqinr_3.4-5
[64] biomaRt_2.38.0 futile.options_1.0.1 XML_3.98-1.16
[67] lambda.r_1.2.3 BiocManager_1.30.4 idr_1.2
[70] httpuv_1.4.5 assertthat_0.2.0 mime_0.6
[73] preseqR_4.0.0 xtable_1.8-3 AnnotationFilter_1.6.0
[76] later_0.7.5 survival_2.42-6 ChIPpeakAnno_3.16.1
[79] memoise_1.1.0 interactiveDisplayBase_1.20.0
