Hi! I already asked this, but was combined with another question, therefore I missed the answer I was looking.
I have my DeseqDataSet which I want to put in Reporting tools -> dds
out <- "/mnt/out/" des2ReportAll <- HTMLReport(shortName = 'RNAseq_analysis_with_DESeq2', title = 'sRNA-seq using DESeq2, pvalue cutoff None', basePath = out, reportDirectory = 'html/') publish(dds, des2ReportAll, pvalueCutoff=2, annotation.db="org.Hs.egENSEMBL", coef = 3,factor = colData(dds)$condition, reportDir=out, n = length(row.names(dds))) #.modifyDF=makeDESeqDF) ##I tried this for the results(dds) but did not work
This is what I use for creating the html report. I would like to include every single gene from the dds into my html (not from the result, because i would like the normalized countings ploted and not the FC), therefore I do not want to filter via pvalue or anything, I would like to have the report of everything. I am wondering where can I specify this.
> sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  ReportingTools_2.12.2 knitr_1.13 pheatmap_1.0.8 stringr_1.0.0  RColorBrewer_1.1-2 DESeq2_1.12.3 SummarizedExperiment_1.2.3 GenomicRanges_1.24.2  GenomeInfoDb_1.8.1 ggplot2_2.1.0 geneplotter_1.50.0 annotate_1.50.0  XML_3.98-1.4 lattice_0.20-33 genefilter_1.54.2 AnnotationDbi_1.34.3  IRanges_2.6.1 S4Vectors_0.10.1 Biobase_2.32.0 BiocGenerics_0.18.0  scatterplot3d_0.3-37 loaded via a namespace (and not attached):  httr_1.2.0 edgeR_3.14.0 AnnotationHub_2.4.2  splines_3.3.0 R.utils_2.3.0 Formula_1.2-1  shiny_0.13.2 interactiveDisplayBase_1.10.3 latticeExtra_0.6-28  RBGL_1.48.1 BSgenome_1.40.1 Rsamtools_1.24.0  Category_2.38.0 RSQLite_1.0.0 biovizBase_1.20.0  limma_3.28.10 chron_2.3-47 digest_0.6.9  XVector_0.12.0 colorspace_1.2-6 ggbio_1.20.1  R.oo_1.20.0 httpuv_1.3.3 htmltools_0.3.5  Matrix_1.2-6 plyr_1.8.4 OrganismDbi_1.14.1  GSEABase_1.34.0 biomaRt_2.28.0 zlibbioc_1.18.0  xtable_1.8-2 GO.db_3.3.0 scales_0.4.0  BiocParallel_1.6.2 PFAM.db_3.3.0 GenomicFeatures_1.24.2  nnet_7.3-12 mime_0.4 survival_2.39-4  magrittr_1.5 R.methodsS3_1.7.1 GGally_1.1.0  hwriter_1.3.2 foreign_0.8-66 GOstats_2.38.0  BiocInstaller_1.22.3 graph_1.50.0 tools_3.3.0  data.table_1.9.6 munsell_0.4.3 locfit_1.5-9.1  cluster_2.0.4 ensembldb_1.4.6 Biostrings_2.40.2  grid_3.3.0 RCurl_1.95-4.8 dichromat_2.0-0  VariantAnnotation_1.18.1 AnnotationForge_1.14.2 bitops_1.0-6  gtable_0.2.0 DBI_0.4-1 reshape_0.8.5  reshape2_1.4.1 R6_2.1.2 GenomicAlignments_1.8.3  gridExtra_2.2.1 rtracklayer_1.32.1 Hmisc_3.17-4  stringi_1.1.1 Rcpp_0.12.5 rpart_4.1-10  acepack_1.3-3.3