Qsea - plotCoverage
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Entering edit mode
@gaurav4thareja-22977
Last seen 20 months ago

Hi Matthias,

I am getting below error while running the plotCoverage function:

plotCoverage(qseaSet, samples=getSampleNames(qseaSet), chr=20, start=29243001, end=29243250, norm_method="beta", col=rep(c("red", "green"), 16), yoffset=1,space=.1, cex=.7 )

selecting specified Region selecting specified ROIs obtaining raw values for 32 samples in 1 windows deriving beta values... Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent

Regards

Gaurav

R version 3.6.0 (2019-04-26) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LC
MONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8 LCPAPER=enUS.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] Haplin7.2.2 pbatR2.2-13
[3] MEDIPSData1.22.0 biomaRt2.42.1
[5] MEDIPS1.38.0 Rsamtools2.2.3
[7] GenomicDataCommons1.10.0 magrittr1.5
[9] BiocParallel1.20.1 BSgenome.Hsapiens.NCBI.GRCh381.3.1000 [11] BSgenome1.54.0 rtracklayer1.46.0
[13] Biostrings2.54.0 XVector0.26.0
[15] GenomicRanges1.38.0 GenomeInfoDb1.22.1
[17] IRanges2.20.2 S4Vectors0.24.4
[19] BiocGenerics0.32.0 qsea1.12.0

loaded via a namespace (and not attached): [1] nlme3.1-147 bitops1.0-6 matrixStats0.56.0
[4] bit64
0.9-7 progress1.2.2 httr1.4.1
[7] tools3.6.0 R62.4.1 DBI1.1.0
[10] mgcv
1.8-31 DNAcopy1.60.0 tidyselect1.0.0
[13] prettyunits1.1.1 bit1.1-15.2 curl4.3
[16] compiler
3.6.0 preprocessCore1.48.0 cli2.0.2
[19] Biobase2.46.0 xml21.3.1 DelayedArray0.12.3
[22] readr
1.3.1 askpass1.1 rappdirs0.3.1
[25] stringr1.4.0 digest0.6.25 pkgconfig2.0.3
[28] highr
0.8 dbplyr1.4.2 limma3.42.2
[31] rlang0.4.5 rstudioapi0.11 RSQLite2.2.0
[34] zoo
1.8-7 jsonlite1.6.1 gtools3.8.2
[37] dplyr0.8.5 RCurl1.98-1.1 GenomeInfoDbData1.2.2
[40] Matrix
1.2-18 Rcpp1.0.4.6 fansi0.4.1
[43] lifecycle0.2.0 stringi1.4.6 MASS7.3-51.5
[46] SummarizedExperiment
1.16.1 rootSolve1.8.2 zlibbioc1.32.0
[49] HMMcopy1.28.1 BiocFileCache1.10.2 grid3.6.0
[52] blob
1.2.1 crayon1.3.4 lattice0.20-41
[55] splines3.6.0 hms0.5.3 knitr1.28
[58] pillar
1.4.3 tcltk3.6.0 ffbase0.12.8
[61] fastmatch1.1-0 XML3.99-0.3 glue1.4.0
[64] data.table
1.12.8 vctrs0.2.4 openssl1.4.1
[67] purrr0.3.3 tidyr1.0.2 assertthat0.2.1
[70] xfun
0.13 ff2.2-14 survival3.1-12
[73] tibble3.0.0 GenomicAlignments1.22.1 AnnotationDbi1.48.0
[76] memoise
1.1.0 ellipsis_0.3.0

Qsea • 244 views
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Entering edit mode
@matthias-lienhard-6292
Last seen 8 months ago
Max Planck Institute for molecular Gene…

Hi Gaurav, plotCoverage is intended to plot more than one window - apparently the issue arises as R collapses the matrix to a vector, as you selected only one row. Can you try to depict more than one window?

Best, Matthias

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Entering edit mode
@matthias-lienhard-6292
Last seen 8 months ago
Max Planck Institute for molecular Gene…

Hi Gaurav, plotCoverage is intended to plot more than one window - apparently the issue arises as R collapses the matrix to a vector, as you selected only one row. Can you try to depict more than one window?

Best, Matthias

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