Hi,
First of all, thank you very much for your interesting and useful package for regulatory network inference.
I had a problem when running runSCENIC_2_createRegulons as described below:
scenicOptions <- runSCENIC_2_createRegulons(scenicOptions)
11:15 Step 2. Identifying regulons
Using the column 'features' as feature index for the ranking database.
Using the column 'features' as feature index for the ranking database.
tfModulesSummary:
[,1]
top50perTargetAndtop50 1
top50perTargetAndtop1sd 3
w0.001Andtop50perTarget 9
top50Andtop1sd 11
w0.005Andtop50 12
w0.005Andtop3sd 15
w0.005Andtop1sd 16
top50Andtop3sd 64
w0.005 71
top5perTarget 73
top10perTarget 97
top50perTarget 182
top3sd 265
top50 358
top1sd 459
w0.001 511
11:15 RcisTarget: Calculating AUC
Using the column 'features' as feature index for the ranking database.
Scoring database: [Source file: hg19-500bp-upstream-7species.mc9nr.feather]
Using the column 'features' as feature index for the ranking database.
Scoring database: [Source file: hg19-tss-centered-10kb-7species.mc9nr.feather]
16:36 RcisTarget: Adding motif annotation
Using BiocParallel...
Using BiocParallel...
Number of motifs in the initial enrichment: 1245640
Number of motifs annotated to the matching TF: 2949
16:42 RcisTarget: Pruning targets
Using the column 'features' as feature index for the ranking database.
Using the column 'features' as feature index for the ranking database.
Error in match.arg(method) : 'arg' must be of length 1
In addition: There were 29 warnings (use warnings() to see them)
warnings()
Warning messages:
1: In eval(formal.args[[as.character(substitute(arg))]], ... :
restarting interrupted promise evaluation
2: In serialize(data, node$con) :
'package:stats' may not be available when loading
3: In serialize(data, node$con) :
'package:stats' may not be available when loading
4: In serialize(data, node$con) :
'package:stats' may not be available when loading
5: In serialize(data, node$con) :
'package:stats' may not be available when loading
6: In serialize(data, node$con) :
'package:stats' may not be available when loading
7: In serialize(data, node$con) :
'package:stats' may not be available when loading
8: In serialize(data, node$con) :
'package:stats' may not be available when loading
9: In serialize(data, node$con) :
'package:stats' may not be available when loading
10: In serialize(data, node$con) :
'package:stats' may not be available when loading
11: In serialize(data, node$con) :
'package:stats' may not be available when loading
12: In serialize(data, node$con) :
'package:stats' may not be available when loading
13: In serialize(data, node$con) :
'package:stats' may not be available when loading
14: In serialize(data, node$con) :
'package:stats' may not be available when loading
15: In serialize(data, node$con) :
'package:stats' may not be available when loading
16: In serialize(data, node$con) :
'package:stats' may not be available when loading
17: In serialize(data, node$con) :
'package:stats' may not be available when loading
18: In serialize(data, node$con) :
'package:stats' may not be available when loading
19: In serialize(data, node$con) :
'package:stats' may not be available when loading
20: In serialize(data, node$con) :
'package:stats' may not be available when loading
21: In serialize(data, node$con) :
'package:stats' may not be available when loading
22: In serialize(data, node$con) :
'package:stats' may not be available when loading
23: In serialize(data, node$con) :
'package:stats' may not be available when loading
24: In serialize(data, node$con) :
'package:stats' may not be available when loading
25: In serialize(data, node$con) :
'package:stats' may not be available when loading
26: In serialize(data, node$con) :
'package:stats' may not be available when loading
27: In serialize(data, node$con) :
'package:stats' may not be available when loading
28: In serialize(data, node$con) :
'package:stats' may not be available when loading
29: In serialize(data, node$con) :
'package:stats' may not be available when loading
I couldn't figure out how to solve the problem yet.
I appreciate any ideas to fix it. Thank you!!
Hi, First of all, thank you very much for your interesting and useful package for regulatory network inference. I had a problem when running runSCENIC_2_createRegulons as described below:
scenicOptions <- runSCENIC_2_createRegulons(scenicOptions) 11:15 Step 2. Identifying regulons Using the column 'features' as feature index for the ranking database. Using the column 'features' as feature index for the ranking database. tfModulesSummary: [,1] top50perTargetAndtop50 1 top50perTargetAndtop1sd 3 w0.001Andtop50perTarget 9 top50Andtop1sd 11 w0.005Andtop50 12 w0.005Andtop3sd 15 w0.005Andtop1sd 16 top50Andtop3sd 64 w0.005 71 top5perTarget 73 top10perTarget 97 top50perTarget 182 top3sd 265 top50 358 top1sd 459 w0.001 511 11:15 RcisTarget: Calculating AUC Using the column 'features' as feature index for the ranking database. Scoring database: [Source file: hg19-500bp-upstream-7species.mc9nr.feather] Using the column 'features' as feature index for the ranking database. Scoring database: [Source file: hg19-tss-centered-10kb-7species.mc9nr.feather] 16:36 RcisTarget: Adding motif annotation Using BiocParallel... Using BiocParallel... Number of motifs in the initial enrichment: 1245640 Number of motifs annotated to the matching TF: 2949 16:42 RcisTarget: Pruning targets Using the column 'features' as feature index for the ranking database. Using the column 'features' as feature index for the ranking database. Error in match.arg(method) : 'arg' must be of length 1 In addition: There were 29 warnings (use warnings() to see them) warnings() Warning messages: 1: In eval(formal.args[[as.character(substitute(arg))]], ... : restarting interrupted promise evaluation 2: In serialize(data, node$con) : 'package:stats' may not be available when loading 3: In serialize(data, node$con) : 'package:stats' may not be available when loading 4: In serialize(data, node$con) : 'package:stats' may not be available when loading 5: In serialize(data, node$con) : 'package:stats' may not be available when loading 6: In serialize(data, node$con) : 'package:stats' may not be available when loading 7: In serialize(data, node$con) : 'package:stats' may not be available when loading 8: In serialize(data, node$con) : 'package:stats' may not be available when loading 9: In serialize(data, node$con) : 'package:stats' may not be available when loading 10: In serialize(data, node$con) : 'package:stats' may not be available when loading 11: In serialize(data, node$con) : 'package:stats' may not be available when loading 12: In serialize(data, node$con) : 'package:stats' may not be available when loading 13: In serialize(data, node$con) : 'package:stats' may not be available when loading 14: In serialize(data, node$con) : 'package:stats' may not be available when loading 15: In serialize(data, node$con) : 'package:stats' may not be available when loading 16: In serialize(data, node$con) : 'package:stats' may not be available when loading 17: In serialize(data, node$con) : 'package:stats' may not be available when loading 18: In serialize(data, node$con) : 'package:stats' may not be available when loading 19: In serialize(data, node$con) : 'package:stats' may not be available when loading 20: In serialize(data, node$con) : 'package:stats' may not be available when loading 21: In serialize(data, node$con) : 'package:stats' may not be available when loading 22: In serialize(data, node$con) : 'package:stats' may not be available when loading 23: In serialize(data, node$con) : 'package:stats' may not be available when loading 24: In serialize(data, node$con) : 'package:stats' may not be available when loading 25: In serialize(data, node$con) : 'package:stats' may not be available when loading 26: In serialize(data, node$con) : 'package:stats' may not be available when loading 27: In serialize(data, node$con) : 'package:stats' may not be available when loading 28: In serialize(data, node$con) : 'package:stats' may not be available when loading 29: In serialize(data, node$con) : 'package:stats' may not be available when loading
I couldn't figure out how to solve the problem yet. I appreciate any ideas to fix it. Thank you!!