search

aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
394 stars 94 forks source link

what is the difference between "motifAnnotations" and "motifAnnotations_hgnc_v9" , and what impact will it have on the results? #447

Open Chenchen3Chen opened 3 months ago

Chenchen3Chen commented 3 months ago

I'm sorry, I'm still new to SCENIC and RStudio.

when I was running it on RStudio , it always reported following error when creating scenicOptions.

Report error: Motif databases selected: hg19-500bp-upstream-7species.mc9nr.feather hg19-tss-centered-10kb-7species.mc9nr.feather Error in eval(as.name(motifAnnotName)) : object 'motifAnnotations_hgnc' not found;

After Report error; NitializeScenic did create the object (object_name is "motifAnnotations") will appear in Environment of RStudio. Then all I had to do was

           motifAnnotations_hgnc <- motifAnnotations

then run initializeScenic again. The code runs smoothly.

However, I see that others can also run it through annother line of code.

code: data(list="motifAnnotations_hgnc_v9", package="RcisTarget")

             motifAnnotations_hgnc <- motifAnnotations_hgnc_v9

The two objects "motifAnnotations" and "motifAnnotations_hgnc_v9" are different in Environment of RStudio;

1111

Therefore, I am very confused about the differences between these two methods, and which method is better to use.

I would really appreciate it if any one can give some suggestions.