search

meichendong / SCDC

SCDC
42 stars 9 forks source link

prepare data from single cell objects for multiple subjects? #23

Open complexgenome opened 3 years ago

complexgenome commented 3 years ago

hi scdc team,

Thank you for the tool. I am interested in using your tool to perform deconvolution on bulk rna sequencing data (in-house) and single-cell from publicly available repositories.

I have single-cell object per subject. The input needed is one object with multiple subjects. However, the tutorial, nor paper mentions how to make one object from different single-cell object.

Is there any guidance on how to combine/merge one expression object from multiple subjects? Is it a list?

I was able to run deconvolution using single subject single-cell object with SCDC_prop_ONE function.

meichendong commented 3 years ago

Hi @sariya , Sorry for the late response. If the subjects are from the same study, then you could first put the expression data matrix together by doing rbind() or cbind(). Then for the pheno data, please create another data.frame to store the matching subjects info / other information for the combined matrix. Then you may follow the way to create a ExpressionSet object. Or like the function getESET() provided by SCDC. Please let me know if this solves your problem. I will be glad to help if you have further questions. Feel free to email: meichen@live.unc.edu

Best, Meichen