tuteja-lab / tissueenrich Goto Github PK
View Code? Open in Web Editor NEWR package for tissue-specific gene enrichment
License: Other
R package for tissue-specific gene enrichment
License: Other
Hi Ashish,
I'm trying to create a custom TissueEnrich dataset but having an issue with the teGeneRetrieval
. Specifically, my commands are:
> head(test[,1:7])
CTBs EPI EVTs Hypoblast ICM PSA.EPI STBs
A4GALT 28.256089 87.818451 9.739999 35.0449376 124.365134 14.0052407 3.8816029
AAAS 166.393659 176.695678 169.025785 166.5609337 178.972602 54.4752599 73.8415541
AACS 3.705388 10.217619 8.844224 11.4724415 5.290590 4.9312505 3.2401403
AADACL2 13.170123 2.072885 16.220174 0.5474843 2.843561 3.5183490 18.3895300
AADACL2-AS1 9.378275 3.074869 8.883682 0.6346828 3.913311 4.3598354 11.7280428
AADACL3 3.670026 5.607436 26.660207 36.3240296 5.195383 0.4045552 0.2788972
> test <- test[,1:7]
> se<-SummarizedExperiment(assays = SimpleList(as.matrix(test)),rowData = row.names(test),colData = colnames(test))
> te.dataset.xiang <-teGeneRetrieval(se)
Error in if (sum(idx) > 0) { : missing value where TRUE/FALSE needed
Could you please help me fix this?
Thanks!
I found although many genes are identified as tissue-specific in my list, there is no significant P-value. I guess the number of tissue-specific genes in that category is very large. But is there any way I can check the number or the genes in each tissue-specific genes category? Thanks!
Hi,
Can I ask what is the foundamental difference between tissue-specific gene enrichment and TWAS (http://gusevlab.org/projects/fusion/)?
Thanks!
best regards,
Jie HUANG, MD MPH PhD
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