Add data documentation

[LouisLeNezet]

Each data file need to be name correctly and documentation should be updated to data.R

• GEX5line.txt
• InputData_for_Survival_v1.txt
• L29_vitro_Control_vs_knockdown_diff.txt
• Limma.csv
• MS_2.rda
• TCGA_CHOL_Clinical_PatientID.txt
• TCGA_CHOL_Expression_PatientID.txt
• autosomes.beta.txt.sorted.chr16
• list_snp_tohighlight.tsv
• pbmc3k.rds
• phenoData.txt
• hg19_chr_list.rda (Louis)

[LouisLeNezet]

Hi everyone !

I would need help on this one.
For each dataset that you would like to include inside the package we need to have a documentation for each of them.
Could you provide me where did you get each of them and how you proceed them ?

Thanks

[aobermayer4]

I do wonder what the formats of each of these are to see if any similarly formatted can be reduced to just one dataset, or if we could use an existing R package to get the data (how the lung data in plotKM was gathered), or maybe we could just have R generate a randomized dataset in the format that is needed. Also, for what we do keep, depending on the size, converting what is used to an R data object might help with size and load time.

I contributed the TCGA CHOL (Cholangiocarcinoma) data, which was derived from the genomic data commons and Cbioportal. This has an expression matrix and the clinical/phenotype data which also has survival data, so it could be used for the plotKM also. I will have to do some looking into for an exact source.

Should each of them have documentation similar to this: https://github.com/stjude-biohackathon/KIDS23-Team13/blob/main/man/hg19_chr_list.Rd ?

[LouisLeNezet]

That would be great I think to use already available datasets.
That's recommended by bioconductor.
The documentation for the data is generated from the https://github.com/stjude-biohackathon/KIDS23-Team13/blob/main/R/data.R
file.

[aobermayer4]

I see, would we just append onto that document with each dataset?

[LouisLeNezet]

Yes that what I've saw in other packages.

[KMcC73]

Sorry for the delay, I've had some other things come up. The only problem is that the single-cell mitochondrial data is not commonly available, to my knowledge. In this case, it might be best to provide an example file and I just need to read up on what type of documentation is required.

[aobermayer4]

@KMcC73 No worries! It's understandable not all data might not be easily available, but Louis provided this (https://github.com/stjude-biohackathon/KIDS23-Team13/blob/main/R/data.R) as an example to follow for documenting our data

[KMcC73]

Great, thank you! I updated the script for the mtCoverage plot so that it is now interactive, has title input. I wanted to make sure I have the functionality in the correct format/corect script structure, but when I went to look for the initial R plot files that @LouisLeNezet had already structured, I cannot find them. Where should I deposit this update file and where are the old ones for a comparison? Sorry, not well-versed with Github protocol.

[LouisLeNezet]

Hi,

The files when correctly formatted need to be directly at the root of the R folder (not in modules), I've put my examples there.
Concerning the example datasets, the original file should be in data-raw and then cleaned up in the files-to-rda.R and exported to rda file in the data folder.
The best would be to use already public accessible files.