Hello,
I keep getting an error I cannot figure out when I run the runPathwayMetaAnalysis function. Here is the error and my code:
Error in mutate():
ℹ In argument: ID = .data$studlab %>% sapply([, 1).
Caused by error in .data$studlab:
! Column studlab not found in .data.
Run rlang::last_trace() to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)
metaRes <- RCPA::runPathwayMetaAnalysis(
allGSResults %>%
group_by(comparison) %>%
group_split(),
method = "REML"
)
metaRes$name <- metaRes$name$name
metaRes$pathwaySize <- metaRes$pathwaySize$pathwaySize
write.csv(file = file.path(exportDir,"meta-results.csv"), as.data.frame(metaRes), row.names = TRUE)
head(allGSResults)
ID p.value score normalizedScore sampleSize
1 GO:0006811 0.1518987 2.718818 2.718818 6
2 GO:0007157 0.1518987 2.718818 2.718818 6
3 GO:0008104 0.1518987 2.718818 2.718818 6
4 GO:0010975 0.1518987 2.718818 2.718818 6
5 GO:0021707 0.1518987 2.718818 2.718818 6
6 GO:0035249 0.1518987 2.718818 2.718818 6
name pFDR pathwaySize
1 monoatomic ion transport 1 4964
2 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules 1 855
3 protein localization 1 1659
4 regulation of neuron projection development 1 265
5 cerebellar granule cell differentiation 1 47
6 synaptic transmission, glutamatergic 1 1033
comparison method
1 101_vs_0 (Mother Culture) ora
2 101_vs_0 (Mother Culture) ora
3 101_vs_0 (Mother Culture) ora
4 101_vs_0 (Mother Culture) ora
5 101_vs_0 (Mother Culture) ora
6 101_vs_0 (Mother Culture) ora
Thanks!
Hello,
I keep getting an error I cannot figure out when I run the
runPathwayMetaAnalysisfunction. Here is the error and my code:Error in
mutate():ℹ In argument:
ID = .data$studlab %>% sapply([, 1).Caused by error in
.data$studlab:! Column
studlabnot found in.data.Run
rlang::last_trace()to see where the error occurred.There were 50 or more warnings (use warnings() to see the first 50)
Thanks!