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| author | Alexander Kabui | 2021-09-23 15:10:16 +0300 |
|---|---|---|
| committer | Alexander Kabui | 2021-09-23 15:10:16 +0300 |
| commit | 9c221e0d89603acd5412be95650a469824e2ab99 (patch) | |
| tree | caf589995b0a88c926f33fda150fbaa5cd6607cc | |
| parent | fc335fa1394a39d1f9f397cb69c755040ecfc5e1 (diff) | |
| download | genenetwork3-9c221e0d89603acd5412be95650a469824e2ab99.tar.gz | |
check for na powerEst and use a default value
| -rw-r--r-- | scripts/wgcna_analysis.R | 10 |
1 files changed, 9 insertions, 1 deletions
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R index ee749e9..c3b1ac8 100644 --- a/scripts/wgcna_analysis.R +++ b/scripts/wgcna_analysis.R @@ -62,13 +62,21 @@ enableWGCNAThreads() powers <- c(c(1:10), seq(from = 12, to=20, by=2)) sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5) +# check the power estimate + +if (is.na(sft$powerEstimate)){ + powerEst = 1 +}else{ + powerEst = sft$powerEstimate +} + # pass user options network <- blockwiseModules(dataExpr, #similarity matrix options corType = corType, #adjacency matrix options - power = 5, + power = powerEst, networkType = "unsigned", #TOM options TOMtype = TOMtype, |