search

xuranw / MuSiC

Multi-subject Single Cell Deconvolution
https://github.com/xuranw/MuSiC
GNU General Public License v3.0
231 stars 92 forks source link

Tutorial: IEmarkers.Rdata #43

Open DSJM opened 4 years ago

DSJM commented 4 years ago

Hello,

sadly loading the Rdata file does result in two character-lists and not one RObject.

Best

tpx888 commented 4 years ago

In Xuran`s tutorial, IEmarkers represents a list of Immune cell and Epith cell marker, you need to create a list object including Epith.marker and Immune.marker which download from the last file of this page "https://xuranw.github.io/MuSiC/articles/pages/data.html" , An IEmarkers.RData. After you create a list object that i mentioned above, you should name the list , Epith.marker "C3", Immune.marker "C4", Then, you need to edit "clusters.type", and remove "C1", and "C2“ form list object "clusters.type" .

yingyonghui commented 3 years ago

In Xuran`s tutorial, IEmarkers represents a list of Immune cell and Epith cell marker, you need to create a list object including Epith.marker and Immune.marker which download from the last file of this page "https://xuranw.github.io/MuSiC/articles/pages/data.html" , An IEmarkers.RData. After you create a list object that i mentioned above, you should name the list , Epith.marker "C3", Immune.marker "C4", Then, you need to edit "clusters.type", and remove "C1", and "C2“ form list object "clusters.type" .

HI, @tpx888 I came up with the same question. according to the tutorial, if I remove "C1", and "C2“ form list object "clusters.type" , I can only get the proportion of "C3" and "C4", which is not my purpose, since I want to deconvolute all cell types in my bulk data. Could you please me some suggestions?

Best, Yonghui