saeyslab/brainimmuneatlas

Overview of the scripts used to analyse the brainimmuneatlas data

brainimmuneatlas's Issues

Label_1 and Label_2

Dear Saeys Lab,
I am trying to work through the code that you posted for your single cell analysis, but unfortunately I'm having some trouble with the the lines

metaData<-data.frame("staticNr"=colnames(rawData), "orig.ident"=label_1, "nGene"=sce$total_features_by_counts, "nUMI"=sce$total_counts, "percent.mito"=sce$pct_counts_Mt, stringsAsFactors = F)

and

metaData[grep('-2',rownames(metaData)), which(colnames(metaData)=="orig.ident")]<-label_2

I'm guessing that these lines refer to objects label_1 and label_2 that denote the origin of the single cell data (i.e. APP/PS1, WT, etc.), but since I don't have access to those objects I can't run the rest of your code. Any chance you could help me figure this out? Thanks, and have a nice day.

calculateQCMetrics() metrics function is depreciated

Tried to get
calculateQCMetrics() metrics function is depreciated.
So this command from line 66 does not work:
sce <- calculateQCMetrics(sce, feature_controls=list(Mt=is.mito))
and produces the following error message:
"Warning message:
'calculateQCMetrics' is deprecated.
Use 'perCellQCMetrics' or 'perFeatureQCMetrics' instead. "

To try and replicate its output I'm using
sce <-AddPerCellQCMetrics(sce)
and sce <- addPerFeatureQC(sce, subsets=is.mito)
so I also added this after line 63 :
names(is.mito)<- rownames(sce)
because unnamed vectors could not be used.

Any feedback on this or on the other issue raised would be really appreciated!