How to deploy a shiny app: https://datasciencegenie.com/how-to-embed-a-shiny-app-on-website/

For review, see:

• CompareDEGenesByMethod.Rmd - can build it
• CompareDEGenesByMethod.pdf - makes sense, typos aren't too bad (meaning: it's understandable)
• results/CvT-compare-SL5.txt - check number of rows, NA values make sense, SL5 has extra column indicating SL4 gene name, if available
• results/CvT-compare-SL4.txt - check number of rows, NA values make sense

Testing:

• Build: Ran the mark down through each chunk and then also knitted and had no issues/errors.
• Comprehension: Markdown makes sense and explains perfectly what the goal and results are.
• SL5 Output: there is an issue with the description column for the output file. It seems it might just be a placement issue within the data frame. SL4 column seems to be holding the description and missing just the gene names for SL4.
• SL4 Output: there is an issue with the description column for the output file. It seems it might just be a placement issue within the data frame. Description isn't present in the output file at all.

Note: When I check bitbucket the output files on there do not have the description issue so I am going to retry updating my fork and rerunning. After comparing the output files it seems mine is showing a basemean column and the one on bitbucket is not which is why the description columns are not in the right place

I went ahead and cloned the main repo and did run into the same issue. Might need to try on another computer to see if this is an output issue only for me or for everyone.

Moving back to to do!

Thanks Molly! I will fix as noted in previous comment.

The SL4 data file appears to be fine. I checked it with:

> fn="results/CvT-compare-SL4.txt"
> d = read.csv(fn,header = T,quote = "",sep="\t")
> names(d)
 [1] "gene"          "group1"        "group2"        "padj.edgeR"    "pvalue.edgeR" 
 [6] "logFC.edgeR"   "padj.DESeq2"   "pvalue.DESeq2" "logFC.DESeq2"  "description"  

I checked the SL5 output file with:

> fn="results/CvT-compare-SL5.txt"
> d = read.csv(fn,header = T,quote = "",sep="\t")
> names(d)
 [1] "gene"          "group1"        "group2"        "padj.edgeR"    "pvalue.edgeR" 
 [6] "logFC.edgeR"   "padj.DESeq2"   "pvalue.DESeq2" "logFC.DESeq2"  "description"  
[11] "SL4"

Example data rows for the SL5 data:

> d$description[1:4]
[1] "Complex 1 LYR protein (AHRD V3.3 *** A0A2U1NHM6_ARTAN) ITAG4.0:Solyc02g085937.1"
[2] "Complex 1 LYR protein (AHRD V3.3 *** A0A2U1NHM6_ARTAN) ITAG4.0:Solyc02g085937.1"
[3] "LeHSP110/ClpB heat shock protein ITAG4.0:Solyc02g088610.4"                      
[4] NA                                                                               
> d$SL4[1:4]
[1] "Solyc02g085937.1" "Solyc02g085937.1" "Solyc02g088610.4" NA       

The files look right to me. Moving this forward to "Needs Testing" for [~molly] to take another look.

Everything looks good now! Moving to done!