The.Works: The.Works
In jbisanz/MicrobeR: Handy functions for microbiome analysis in R
Description
Usage
Arguments
Value
Description
Takes a feature/OTU/SV table and calculates an extensive set of metrics for downstream use. A number of versions of the normalized data are available from the returned object. See below for more information. For extremely large tables (>500x1000) this function is not reccomended as it will make numerous copies and have a significant memory footprint.
Usage
1
Values<-TheWorks(MicrobeR.Demo.SVtable,MicrobeR.Demo.Tree)
Arguments
FEATURES
Table of feature/OTU/SV counts where Samples are columns, and IDs are row names.
TREE
A phylogenetic tree for UniFrac and phylogenetic distances.
VERBOSE
Should progress and metrics be printed to screen via message()? Default=TRUE
Value
A named list containing the following:
.$Features$RawCounts- The original input file of raw counts
.$Features$subsampled- A table of counts sampled to the lowest read count
.$Features$Filtered- Counts where features present in less than 3 samples with less than 10 reads were removed
.$Features$CLR- A CLR-normalized table (see Make.CLR)
.$Features$Percent- The features as percent abundance (sum to 100)
.$Features$Proportion- The feature as straight proportions (sum to 1)
.$Features$PhILR- The Phylogenetic isometric log ratio transform (see package information for philr)
.$Features$Tree$Raw- The input Tree
.$Tree$... The corresponding pruned trees for the feature tables aboeve
.$AlphaDiversity- A number of alpha diversity metrics in a data frame
.$DistanceMatrices- A named list of distance matrices for UniFrac (w/uw), bray curtis, jsd, jaccard, PhILR euclidian, and CLR euclidian
.$PCoA$Vectors- A named list numeric coordinates for plotting PCoA analysis
.$PCoA$Scree- A table containing the percent variation explained for all calculated distance matrices to help in selecting the most appropriate metric.
jbisanz/MicrobeR documentation built on June 5, 2019, 7:53 p.m.
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Description Usage Arguments Value
Description
Takes a feature/OTU/SV table and calculates an extensive set of metrics for downstream use. A number of versions of the normalized data are available from the returned object. See below for more information. For extremely large tables (>500x1000) this function is not reccomended as it will make numerous copies and have a significant memory footprint.
Usage
1 | Values<-TheWorks(MicrobeR.Demo.SVtable,MicrobeR.Demo.Tree)
|
Arguments
FEATURES |
Table of feature/OTU/SV counts where Samples are columns, and IDs are row names. |
TREE |
A phylogenetic tree for UniFrac and phylogenetic distances. |
VERBOSE |
Should progress and metrics be printed to screen via message()? Default=TRUE |
Value
A named list containing the following:
.$Features$RawCounts- The original input file of raw counts
.$Features$subsampled- A table of counts sampled to the lowest read count
.$Features$Filtered- Counts where features present in less than 3 samples with less than 10 reads were removed
.$Features$CLR- A CLR-normalized table (see Make.CLR)
.$Features$Percent- The features as percent abundance (sum to 100)
.$Features$Proportion- The feature as straight proportions (sum to 1)
.$Features$PhILR- The Phylogenetic isometric log ratio transform (see package information for philr)
.$Features$Tree$Raw- The input Tree
.$Tree$... The corresponding pruned trees for the feature tables aboeve
.$AlphaDiversity- A number of alpha diversity metrics in a data frame
.$DistanceMatrices- A named list of distance matrices for UniFrac (w/uw), bray curtis, jsd, jaccard, PhILR euclidian, and CLR euclidian
.$PCoA$Vectors- A named list numeric coordinates for plotting PCoA analysis
.$PCoA$Scree- A table containing the percent variation explained for all calculated distance matrices to help in selecting the most appropriate metric.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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