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Old 04-11-2014, 02:07 PM   #1
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Location: New York

Join Date: Apr 2014
Posts: 1
Default deepSNV summary of all positions

Dear all

I would like to make a summary of every row of a deepSNV object, especially the counts in the forward/reverse direction.


> library(deepSNV)
> data(HIVmix)
> nrow(test(HIVmix))
[1] 1512

> summ <- summary(HIVmix, fold.change=-1000000, sig.level=0.5, adjust.method=NULL )
> nrow(summ)
[1] 770

> summ <- summary(HIVmix, fold.change=-1000000, sig.level=1, adjust.method=NULL )
Error in data.frame(chr = deepSNV@regions$chr[reg_ix], pos = pos, ref = CV.control[cond.rows], :
arguments imply differing number of rows: 2634, 6048

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] deepSNV_1.8.0 VGAM_0.9-3 VariantAnnotation_1.8.13 Rsamtools_1.14.3 AnnotationHub_1.2.0 methVisual_1.14.0 plotrix_3.5-5
[8] sqldf_0.4-7.1 RSQLite.extfuns_0.0.1 gsubfn_0.6-5 proto_0.3-10 ca_0.53 gridBase_0.4-7 Biostrings_2.30.1
[15] shiny_0.9.1 devtools_1.4.1 DEXSeq_1.8.0 mgcv_1.7-28 nlme_3.1-115 cummeRbund_2.4.1 Gviz_1.6.0
[22] rtracklayer_1.22.6 fastcluster_1.1.13 RSQLite_0.11.4 DBI_0.2-7 DAVIDQuery_1.22.0 RCurl_1.95-4.1 bitops_1.0-6
[29] BiocInstaller_1.12.0 biomaRt_2.18.0 ArrayTools_1.22.0 affy_1.40.0 Biobase_2.22.0 DESeq2_1.2.10 RcppArmadillo_0.
[36] Rcpp_0.11.1 reshape2_1.2.2 plyr_1.8.1 GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 BiocGenerics_0.8.0
[43] VennDiagram_1.6.5 colorfulVennPlot_2.4 scales_0.2.3 ggplot2_0.9.3.1

loaded via a namespace (and not attached):
[1] affyio_1.30.0 annotate_1.40.1 AnnotationDbi_1.24.0 biovizBase_1.10.8 BSgenome_1.30.0 caTools_1.16 chron_2.3-45 cluster_1.15.1
[9] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 evaluate_0.5.1 Formula_1.1-1 genefilter_1.44.0 GenomicFeatures_1.14.5 gtable_0.1.2
[17] Hmisc_3.14-3 httpuv_1.2.3 httr_0.2 hwriter_1.3 labeling_0.2 lattice_0.20-27 latticeExtra_0.6-26 limma_3.18.13
[25] locfit_1.5-9.1 MASS_7.3-30 Matrix_1.1-2-2 memoise_0.1 munsell_0.4.2 preprocessCore_1.24.0 RColorBrewer_1.0-5 rjson_0.2.13
[33] RJSONIO_1.0-3 statmod_1.4.18 stringr_0.6.2 survival_2.37-7 tools_3.0.2 whisker_0.3-2 XML_3.95-0.2 xtable_1.7-3
[41] zlibbioc_1.8.0
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