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Hello. I am attempting to integrate two merged objects, one sci-atac the other snRNA, and having an issue while calculating gene activity. Despite the error it appears the chromosomes in the frag files are consistent with the annotations. Not sure if I need to merge fragment files for the atac component as in the 0.2.5 signac merging vignette. It seems that method was phased out. Any advice would be appreciated. Thanks!
Here is the code and traceback.
gene.activities <- GeneActivity(atac.sobj, features = VariableFeatures(atac.sobj))
1. GeneActivity(atac.sobj, features = VariableFeatures(atac.sobj))
2. FeatureMatrix(fragments = frags, features = transcripts, cells = cells,
. verbose = verbose, ...)
3. sapply(X = obj.use, FUN = function(x) {
. SingleFeatureMatrix(fragment = fragments[[x]], features = features,
. cells = cells, sep = sep, verbose = verbose, process_n = process_n)
. })
4. lapply(X = X, FUN = FUN, ...)
5. FUN(X[[i]], ...)
6. SingleFeatureMatrix(fragment = fragments[[x]], features = features,
. cells = cells, sep = sep, verbose = verbose, process_n = process_n)
7. stop("No matching chromosomes found in fragment file.")
My guess is that VariableFeatures(atac.sobj) is an empty vector, or a set of peak names rather than gene names. I've improved the error checking in the GeneActivity() function to give more informative error messages (on develop branch, see instructions here: https://satijalab.org/signac/articles/install.html#development-version-1)
I see. You are correct VariableFeatures() is returning peaks. I did not realize that was an issue due to peaks being the currently defined feature set in the object. It made sense to me the variable features would be peaks.
In this case how would VariableFeatures be pointed towards the genes present in our annotations vs our peaks?
The features parameter should be a list of gene names present in the gene annotation that you want to quantify, or you can leave it blank to quantify all protein-coding genes in the gene annotation
Hello. I am attempting to integrate two merged objects, one sci-atac the other snRNA, and having an issue while calculating gene activity. Despite the error it appears the chromosomes in the frag files are consistent with the annotations. Not sure if I need to merge fragment files for the atac component as in the 0.2.5 signac merging vignette. It seems that method was phased out. Any advice would be appreciated. Thanks!
Here is the code and traceback.
Here are samples of the annotation and fragments.
Fragment object (one of six present in merged atac object):
Our OS is CentOS. Here is the session info:
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