Generate html report about the analysis of 2’Ome profile
Usage
report_2ome_sites(
ribo,
specie = "not specified",
condition_col,
project_name = "Unnamed project",
output_dir = getwd(),
comments = NULL
)Examples
data('ribo_toy')
data("human_methylated")
ribo_adj_small <- remove_ribo_samples(ribo_toy, c("RNA1","RNA2"))
ribo_adj_small_name <- rename_rna(ribo_adj_small,
new_names = c("5S", "5.8S", "18S", "28S"))
ribo_adj_annot <- annotate_site(ribo_adj_small_name,
annot = human_methylated,
anno_rna = "rRNA",
anno_pos = "Position",
anno_value = "Nomenclature")
report_2ome_sites(ribo = ribo_adj_annot, specie = "human",
condition_col = "condition", project_name = "name", comments = "./comment_2ome_comp1.Rmd")
#>
#>
#> processing file: 2ome_analysis.Rmd
#> 1/39
#> 2/39 [unnamed-chunk-1]
#> 3/39
#> 4/39 [labrary]
#> 5/39
#> 6/39 [unnamed-chunk-2]
#> 7/39
#> 8/39 [prepare metadata table]
#> 9/39
#> 10/39 [print metadata table]
#> 11/39
#> 12/39 [premiere table]
#> 13/39
#> 14/39 [unnamed-chunk-3]
#> 15/39
#> 16/39 [create title and subtitle for the 1st heatmap]
#> 17/39
#> 18/39 [unnamed-chunk-4]
#> 19/39
#> 20/39 [unnamed-chunk-5]
#> 21/39
#> 22/39 [IQR]
#> 23/39
#> 24/39 [unnamed-chunk-6]
#> 25/39
#> 26/39 [plot PCA]
#> 27/39
#> 28/39 [create title and subtitle for the 2nd heatmap]
#> 29/39
#> 30/39 [heatmap mosts variant sites]
#> 31/39
#> 32/39 [summary table]
#> 33/39
#> 34/39 [print last table]
#> 35/39
#> 36/39 [unnamed-chunk-7]
#> 37/39
#> 38/39 [unnamed-chunk-8]
#> 39/39
#> output file: 2ome_analysis.knit.md
#> /opt/hostedtoolcache/pandoc/3.1.11/x64/pandoc +RTS -K512m -RTS 2ome_analysis.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/runner/work/rRMSAnalyzer/rRMSAnalyzer/docs/reference/2ome_analysis.html --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/runner/work/_temp/Library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=cosmo --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp7AaMJc/rmarkdown-str21f74a602f30.html
#>
#> Output created: 2ome_analysis.html