Hello, could you please check if you have successfully Init.DataMeta ?
The mbset should be a list. Usually this message suggest the failure of previous steps which make the mbset to -1.
If mbset hasn’t been initialize successfully, please make sure you have all the related packages installed and use the correct file path.
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Thank you for the reply. But i re-install everything and even checked Init.DataMeta. Everything seems to be working.
When i load the package:
library(MicrobiomeAnalystR)
Loading required package: phyloseq
There were 32 warnings (use warnings() to see them)
warnings()
Warning messages:
1: replacing previous import ‘MASS::area’ by ‘genefilter::area’ when loading ‘MicrobiomeAnalystR’
2: replacing previous import ‘ape::ring’ by ‘igraph::ring’ when loading ‘MicrobiomeAnalystR’
3: replacing previous import ‘ape::edges’ by ‘igraph::edges’ when loading ‘MicrobiomeAnalystR’
4: replacing previous import ‘ape::mst’ by ‘igraph::mst’ when loading ‘MicrobiomeAnalystR’
5: replacing previous import ‘ape::degree’ by ‘igraph::degree’ when loading ‘MicrobiomeAnalystR’
6: replacing previous import ‘ape::complement’ by ‘metacoder::complement’ when loading ‘MicrobiomeAnalystR’
7: replacing previous import ‘igraph::hierarchy’ by ‘metacoder::hierarchy’ when loading ‘MicrobiomeAnalystR’
8: replacing previous import ‘ggplot2::map_data’ by ‘metacoder::map_data’ when loading ‘MicrobiomeAnalystR’
9: replacing previous import ‘edgeR::calcNormFactors’ by ‘metagenomeSeq::calcNormFactors’ when loading ‘MicrobiomeAnalystR’
10: replacing previous import ‘metacoder::filter_taxa’ by ‘phyloseq::filter_taxa’ when loading ‘MicrobiomeAnalystR’
11: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘MicrobiomeAnalystR’
12: replacing previous import ‘gridExtra::combine’ by ‘randomForest::combine’ when loading ‘MicrobiomeAnalystR’
13: replacing previous import ‘data.table::melt’ by ‘reshape::melt’ when loading ‘MicrobiomeAnalystR’
14: replacing previous import ‘metacoder::is_root’ by ‘taxa::is_root’ when loading ‘MicrobiomeAnalystR’
15: replacing previous import ‘metacoder::is_stem’ by ‘taxa::is_stem’ when loading ‘MicrobiomeAnalystR’
16: replacing previous import ‘igraph::as_data_frame’ by ‘taxa::as_data_frame’ when loading ‘MicrobiomeAnalystR’
17: replacing previous import ‘metacoder::n_subtaxa’ by ‘taxa::n_subtaxa’ when loading ‘MicrobiomeAnalystR’
18: replacing previous import ‘metacoder::is_internode’ by ‘taxa::is_internode’ when loading ‘MicrobiomeAnalystR’
19: replacing previous import ‘metacoder::taxon’ by ‘taxa::taxon’ when loading ‘MicrobiomeAnalystR’
20: replacing previous import ‘metacoder::internodes’ by ‘taxa::internodes’ when loading ‘MicrobiomeAnalystR’
21: replacing previous import ‘metacoder::taxon_id’ by ‘taxa::taxon_id’ when loading ‘MicrobiomeAnalystR’
22: replacing previous import ‘metacoder::subtaxa’ by ‘taxa::subtaxa’ when loading ‘MicrobiomeAnalystR’
23: replacing previous import ‘metacoder::n_supertaxa’ by ‘taxa::n_supertaxa’ when loading ‘MicrobiomeAnalystR’
24: replacing previous import ‘metacoder::taxon_rank’ by ‘taxa::taxon_rank’ when loading ‘MicrobiomeAnalystR’
25: replacing previous import ‘metacoder::stems’ by ‘taxa::stems’ when loading ‘MicrobiomeAnalystR’
26: replacing previous import ‘metacoder::leaves’ by ‘taxa::leaves’ when loading ‘MicrobiomeAnalystR’
27: replacing previous import ‘metacoder::n_leaves’ by ‘taxa::n_leaves’ when loading ‘MicrobiomeAnalystR’
28: replacing previous import ‘metacoder::roots’ by ‘taxa::roots’ when loading ‘MicrobiomeAnalystR’
29: replacing previous import ‘metacoder::taxonomy’ by ‘taxa::taxonomy’ when loading ‘MicrobiomeAnalystR’
30: replacing previous import ‘metacoder::supertaxa’ by ‘taxa::supertaxa’ when loading ‘MicrobiomeAnalystR’
31: replacing previous import ‘metacoder::is_leaf’ by ‘taxa::is_leaf’ when loading ‘MicrobiomeAnalystR’
32: replacing previous import ‘igraph::diversity’ by ‘vegan::diversity’ when loading ‘MicrobiomeAnalystR’`
Later When the object is Initiated using Init.mbSetObj()
mbSet <- Init.mbSetObj()
[1] "Init MicrobiomeAnalyst!"`
3. mbSet <- Init.DataMeta(mbSet, F)
Now the mbSet is structured like this
`>mbSet
$dataSet
list()
$analSet
list()
$imgSet
list()
$is.ASV
[1] FALSE
$poor.replicate
[1] FALSE
$tree.uploaded
[1] FALSE
$cmdSet
character(0)
$dataSets
list()
$mdata.all
list()