gnomeR

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 https://docs.cbioportal.org/file-formats/#structural-variant-data

hfuchs5

Create text binary matrix which retains specific mutation type in matrix

16

@edrill suggested this. This can be useful for oncoprints and more in-depth mutation specific analyses. The relevant information seems to be in the following MAF columns: ``` r table(gnomeR::mutations$mutationType, gnomeR::mutations$variantType)...

karissawhiting

gene_binary duplicated IDs

6

Check to make sure duplicate IDs are not allowed in gene_binary and make a test for it

jflynn264

Minor bugs in `create_gene_binary()`

4

Creating one issue with all feedback as not sure what all we want to actually work on for next steps.. ✅**1 As of now, the function will break if the...

akriti21

```r library(dplyr) library(stringr) extract_patient_id % mutate(patient_id = str_replace(sample_id, "-T.*", ""))) } else { # If any value does not match the format, raise an error cli::cli_abort("Some {.code sample_id} values do...

karissawhiting

Test the main package functions with different size maf files to better assess the problem.

hfuchs5

Review Segmentation Functions

1

Currently these are in the `inst` > `seg-stuff` folder. I removed some dependencies that these functions needed for now. We can add them back as needed ({iClusterPlus}, {GenomicRanges}, {lattice}, {iRanges},...

karissawhiting

Gb class internal func

1

**What changes are proposed in this pull request?** added a S3 object called "tbl_gene_binary" to allow functions to identify if data is the proper format, updated many functions to deal...

hfuchs5

karissawhiting

IMPACT Checklist Vignette

3

Create a vignette in {gnomeR} to guide people through IMPACT data checks with explanations and examples - [ ] Decide what data set /samples to use. - [ ] Create...

karissawhiting