salmon-EC - Githubissues

thelovelab / fishpond

Differential expression and allelic analysis, nonparametric statistics

https://thelovelab.github.io/fishpond

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salmon-EC #18

Closed jgilis closed 2 years ago

jgilis commented 2 years ago

Hi Mike,

PR for including salmon-EC, a function to generate an equivalence class (EC) count matrix from salmon output, more specifically from raw eq_classes.txt files that are generated by running salmon with the optional --dumpEq flag.

Just one point of discussion:

In the readEq helper function, I generate the rownames of the ECC matrix. This is done by pasting/collapsing the indices of transcripts with which the ECC is compatible. I previously did this with stringi::stri_c, but now changed it to paste. The latter is a bit slower, but of course avoids having stringi in Suggests. The speed loss for my dataset is approximately 2%.

Best regards,

Jeroen

mikelove commented 2 years ago

Just a note, I made these changes to account for these function definitions below, and I also added salmonEC to the pkgdown list of reference topics.

* checking R code for possible problems ... NOTE
readEq: no visible global function definition for ‘fread’
readEq: no visible binding for global variable ‘last’
salmonEC: no visible global function definition for ‘fread’
salmonEC: no visible global function definition for ‘sparseVector’
sv.cbind: no visible binding for global variable ‘slot’

jgilis commented 2 years ago

Ah great, I indeed forgot about including those! I was supposed to include

@importFrom methods slot @importFrom data.table fread last @importFrom svMisc progress

in the salmonEC imports, but then I forgot. But ofc calling with :: from Suggest is good as well!

mikelove commented 2 years ago

I think we're set. Thanks again for these contributions. I noted some thoughts in #salmon2bioc about test data etc.