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Add data documentation #2
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Hi everyone ! I would need help on this one. Thanks |
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 ? |
That would be great I think to use already available datasets. |
I see, would we just append onto that document with each dataset? |
Yes that what I've saw in other packages. |
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. |
@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 |
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. |
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. |
Each data file need to be name correctly and documentation should be updated to data.R
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