I have a question about the deconvolution method used in the flagship PsychENCODE paper Comprehensive functional genomic resource and integrative model for the human brain. I would like to perform a similar analysis on my own bulk samples using the single cell expression profiles used in the paper, however it is unclear how these profiles are formed.
Specifically, supplementary file DER-23 lists the cell type fractions for 24 cell types. These coefficients presumably came from solving the following:
B = C * W
Where B is the marker gene by samples matrix, C is the marker gene by cell type matrix, and W is the appropriate weights matrix. How do I go about obtaining or reproducing the 24 cell type profiles? From what I can tell, these profiles were not released along with the other supplemental data sets.
If you could please answer my question or forward this email on the appropriate author(s), I would appreciate it.
Sorry for the late reply. I think the profiles you want are on resource.psychencode.org
I am writing in regards to the datasets posted on PsychENCODE website. I noticed that full summary statistics for QTL maps are posted for eQTLs and isoQTLs, but cQTLS and fQTLs only have top SNP information. Is there a chance you could upload full summary stats for cQTLs and fQTLs as well?
We calculated cQTLs and fQTLs differently from eQTLs and isoQTLs. So we only have top SNP information for cQTLs and fQTLs.
Was the eQTLs calculated on 1,886 unique individuals?
No, the eQTLs were calculated on 1387 filtered adult samples with matching gene expression and genotypes.
In Fig S34, it mentions only 1,432 individuals have genotyped. How was the genotype information determined for the remaining 454 individuals?
We didn’t have genotype information determined for the remaining 454 individuals. So we didn’t include these 454 individuals in any QTL analysis.
The # of samples with genotypes enumerated in Table S1 and Table S11 do not appear to match. For example, Table S1 reports 450 GTEx samples (97 DFC), but Table S11 reports 25 GTEx genotypes from the pre-frontal cortex. There might be some subtlety between these two tables I have missed, could you please clarify how to properly interpret these tables?
The Genotypes column in Table S11 only includes the filtered high genotyping quality samples (for example, genotype imputation accuracy score R2>0.3) which have matched RNA-seq data.