question on 6.TF.candidate.R script

[pseudacriscrucifer]

Hi!

Is not an issue - but wanted to ask, what is the meta.rna data, specifically? I understand that rna is the relevant Seurat object, but I cannot find anything in the publication or github on what the second scRNA.meta.0816.rds file is?

Thanks so much!

.libPaths("/net/bmc-lab5/data/kellis/users/xiongxs/R/3.6")
library(Seurat)

# read in RNA-seq data and annotation
library(SingleCellExperiment)
rna = readRDS("/net/bmc-lab5/data/kellis/users/xiongxs/Proj_snATAC_AD/20210205_PFC.reprocess/2.UseArchR.Re2/C.01.rna.marker/RNA.subset.seurat.rds")

# read in the GS-chromVar correlation
cor = read.table('C.16.Positive.TF/TF.motif_vs_exp.correlation.xls',head=T)
tf.list = as.character(cor$GeneScoreMatrix_matchName)

Markers = FetchData(rna,tf.list)   # no 'BHLHA15'; remove it from the other two matrices
meta.rna = readRDS('./scRNA.meta.0816.rds')
meta.rna = meta.rna[rownames(Markers),]
all(rownames(meta.rna) == rownames(Markers))
Markers.mean = aggregate(Markers,list(meta.rna$major.celltype),FUN=mean)
rownames(Markers.mean) = Markers.mean$Group.1
Markers.mean.rna = Markers.mean[,-1]
Markers.mean.rna = Markers.mean.rna[c('Exc','Inh','Ast','Oli','Opc','Mic','Vas'),]```