Feedback on Getting Started Vignette #18
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vignettes/getting-started.Rmd
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| - `id`: an ID corresponding to the names of paired guides | ||
| - `seq_1`: gRNA sequence 1, targeting "paralog A" | ||
| - `seq_2`: gRNA sequence 2, targeting "paralog B" | ||
| - The sample, day, and replicate number for which gRNAs were sequenced (TODO) |
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I was unclear what the last bullet point was saying. The column names in example_data that this point is referencing, Day00_RepA, Day05_RepA, Day22_RepA Day22_RepB Day22_RepC, doesn't seem to have any info on the sample. I think the names refer to the Day, and Replicate number, but not the sample.
I would list out each column and describe what each column is. For ex,
Day00_RepA: Gene Counts from Day 00 for Replicate ADay05_RepA: Gene Counts from Day 05 for Replicate ADay22_RepA: Gene Counts from Day 22 for Replicate ADay22_RepB: Gene Counts from Day 22 for Replicate B
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This also sounds great! Can you add this?
vignettes/getting-started.Rmd
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| @@ -19,24 +19,24 @@ knitr::opts_chunk$set( | |||
| gimap performs analysis of dual-targeting CRISPR screening data, with the goal of aiding the identification of genetic interactions (e.g. cooperativity, synthetic lethality) in models of disease and other biological contexts. gimap analyzes functional genomic data generated by the pgPEN (paired guide RNAs for genetic interaction mapping) approach, quantifying growth effects of single and paired gene knockouts upon application of a CRISPR library. A multitude of CRISPR screen types can be used for this analysis, with helpful descriptions found in this review (https://www.nature.com/articles/s43586-021-00093-4). Use of pgPEN and GI-mapping in a paired gRNA format can be found here (https://pubmed.ncbi.nlm.nih.gov/34469736/). | |||
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| ```{r} | |||
| library(magrittr) | |||
| library(dplyr) | |||
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If we are going to use dplyr, we might as well load dplyr, which loads magrittr.
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Sounds good to me! Can you add this in too?
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@howardbaek I like these suggestions, can you commit them? |
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Hi @howardbaek thanks for bringing up these points and initiating the conversation at the meeting. I left some suggested wordings in this review, feel free to make adjustments for clarity as you see needed. But I think what you started here is great and very much needed!
Thanks!
vignettes/getting-started.Rmd
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| - pg_metadata: paired guide metadata | ||
| - sample_metadata: Metadata of dataset where columns are different samples and rows are different paired guide. | ||
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Probably can delete these extra lines.
Co-authored-by: Candace Savonen <cansav09@gmail.com>
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Is this ready as far as you know @howardbaek ? |
Okay never mind. There's failing checks. Pull up pull up! I'm going to look into them. |
I made a couple minor suggestions to the Getting Started vignette. I'll put additional feedback in inline comments below.