wyguo / ThreeDRNAseq

A pipeline for differential expression and differential alternative splicing analysis
https://github.com/wyguo/ThreeDRNAseq
GNU General Public License v3.0
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"Low.expression.filter" function not found #44

Open MrGoebel opened 1 year ago

MrGoebel commented 1 year ago

First of all, thanks for developing this app.

I'm using the R script of your app. I got through importing the data just fine, but now I'm stuck on the "filter low expression transcripts" part. The "low.expression.filter" function does not seem to exist in any of the used packages. I also could not find any information about it online. Could you let me know, what package this function is part of, or if I'm missing anything else? I'm quite new to R and to coding in general so I hope I'm not just missing some stupid little fix.

For some more context, this is the code passage in question:

##----->> Do the filters
target_high <- low.expression.filter(abundance = trans_counts,
                                     mapping = mapping,
                                     abundance.cut = cpm_cut,
                                     sample.n = cpm_samples_n,
                                     unit = 'counts',
                                     Log=F)

and it returns the following error: Error in low.expression.filter(abundance = trans_counts, mapping = mapping, : could not find function "low.expression.filter"

peterjc commented 1 year ago

Looks like a duplicate of #43 which reports this function and others are missing in a recent installation.