opm: Analysing Phenotype Microarray and Growth Curve Data

Tools for analysing OmniLog(R) and MicroStation(TM) phenotype microarray (PM) data as produced by the devices distributed by BIOLOG Inc. as well as similar kinds of data such as growth curves. Major facilities are plotting data, accurately estimating curve parameters, comparing and discretising data, creating phylogenetic formats and reports for taxonomic journals, drawing the PM analysis results in biochemical pathway graphs optionally including genome annotations, running multiple comparisons of means, easy interaction with powerful feature-selection approaches, integrating metadata, using the YAML format for the storage of data and metadata, batch conversion of large numbers of files, and database I/O.

Author
Markus Goeker, with contributions by Benjamin Hofner, Lea A.I. Vaas, Johannes Sikorski, Maria del Carmen Montero Calasanz, Jan P. Meier-Kolthoff, Nora Buddruhs and Anne Fiebig
Date of publication
2016-11-14 17:03:08
Maintainer
Markus Goeker <markus.goeker@dsmz.de>
License
GPL (>= 2)
Version
1.3.64
URLs

View on R-Forge

Man pages

aggregated
Get aggregated data
annotated
Create vector or matrix with substrate annotation
as.data.frame
Create data frame
batch_opm
Batch-convert PM data
boccuto_et_al
Autism cell-line example data set
bracket
Select subset
bracket.set
Assign subset
c
Combination and addition of plates
ci_plot
Plot point estimates with CIs
collect_template
Input metadata
csv_data
Information from input CSV file
dim
Get dimensions
discrete
Discretisation functions
discretized
Get discretised data
do_aggr
Aggregate kinetics using curve-parameter estimation
do_disc
Discretise curve parameters
duplicated
Determine duplicated plates
explode_dir
Helper functions for file input and output
extract
Extract aggregated values and/or metadata
find_substrate
Identify substrates or positions
has_aggr
Are aggregated or discretised data present?
heat_map
Heat map
html_args
HTML formatting and output label generation
include_metadata
Add or map metadata or edit them by hand
infix.k
Query metadata keys
infix.q
Query metadata
kmeans
Work with k-means results
level_plot
Level plot
max
Overall or minimal maximum
measurements
Stored measurements
merge
Merge or split plates
metadata
Get metadata
metadata.set
Replace metadata
OPM
Real classes of the 'opm' package
OPM_DB
Classes for 'opm' database I/O
opm_dbput
Database I/O for 'opm'
opm_files
Files and colour sets used by the package
opm_mcp
Multiple comparison of group means
opm_opt
Global 'opm' options
opm.package
The 'opm' package
opms.function
OPMS constructor
opmx.function
Convert user-defined objects to OPMX
parallel_plot
Parallel plot
phylo_data
Export phylogenetic data
plates
Get available plates or apply function to them
plate_type
Plate type displayed or modified, registered or deleted
potato
Potato cell-line growth data set
radial_plot
Radial plot
read_opm
Read multiple PM files at once or read single PM file
run_kmeans
Conduct k-means partitioning
separate
Regularly split character vectors if possible
set_spline_options
Spline options
sort
Sort, unify, revert or repeat OPMS objects
subset
Select a subset of the plates (or time points)
substrate_info
Provide information on substrates
summary
Summarise OPMX or MOPMX objects
to_yaml
Convert to YAML
vaas_4
Example data sets from Vaas et al. (2012)
wells
Listing of well names
WMD
Virtual classes of the 'opm' package
xy_plot
X-Y plot

Files in this package

opm/COPYING
opm/ChangeLog
opm/DESCRIPTION
opm/NAMESPACE
opm/NEWS
opm/R
opm/R/aggregation-aux.R
opm/R/aggregation.R
opm/R/auxiliary-aux.R
opm/R/auxiliary.R
opm/R/classes-aux.R
opm/R/classes.R
opm/R/combination-aux.R
opm/R/combination.R
opm/R/constants.R
opm/R/conversion-aux.R
opm/R/conversion.R
opm/R/data.R
opm/R/dbio-aux.R
opm/R/dbio.R
opm/R/discretization.R
opm/R/getter.R
opm/R/imports.R
opm/R/io-aux.R
opm/R/io.R
opm/R/kmeans-aux.R
opm/R/kmeans.R
opm/R/metadata.R
opm/R/multcomp-aux.R
opm/R/multcomp.R
opm/R/naming-aux.R
opm/R/naming.R
opm/R/package.R
opm/R/phylogeny-aux.R
opm/R/phylogeny.R
opm/R/plate-map.R
opm/R/plotting-aux.R
opm/R/plotting.R
opm/R/splinefit-aux.R
opm/R/substrate-info.R
opm/R/testing-aux.R
opm/R/well-map.R
opm/build
opm/build/vignette.rds
opm/data
opm/data/boccuto_et_al.rda
opm/data/potato.rda
opm/data/vaas_1.rda
opm/data/vaas_4.rda
opm/demo
opm/demo/00Index
opm/demo/MongoDB-IO.R
opm/demo/MySQL-IO.R
opm/demo/PostgreSQL-IO.R
opm/demo/SQLite-IO.R
opm/demo/cluster-with-pvalues.R
opm/demo/custom-PCA.R
opm/demo/distinguish-curve-topologies.R
opm/demo/identify-positive-reactions.R
opm/demo/multiple-plate-types.R
opm/demo/phenotype-vs-genotype.R
opm/demo/workshop-part-1.R
opm/demo/workshop-part-2.R
opm/demo/workshop-part-3.R
opm/demo/workshop-part-4.R
opm/demo/workshop-part-5.R
opm/inst
opm/inst/CITATION
opm/inst/auxiliary
opm/inst/auxiliary/001_rdbms_drop.sql
opm/inst/auxiliary/002_rdbms_create.sql
opm/inst/auxiliary/003_rdbms_delete.sql
opm/inst/auxiliary/styles_1.css
opm/inst/doc
opm/inst/doc/opm-growth-curves.Rnw
opm/inst/doc/opm-growth-curves.pdf
opm/inst/doc/opm-substrates.Rnw
opm/inst/doc/opm-substrates.pdf
opm/inst/doc/opm-tutorial.Rnw
opm/inst/doc/opm-tutorial.pdf
opm/inst/scripts
opm/inst/scripts/run_opm.R
opm/inst/testdata
opm/inst/testdata/Example_1.csv.xz
opm/inst/testdata/Example_2.csv.xz
opm/inst/testdata/Example_3.csv.xz
opm/inst/testdata/Example_Ecoplate.csv.xz
opm/inst/testdata/Example_ID_run.csv.xz
opm/inst/testdata/Example_LIMS_Export.exl.xz
opm/inst/testdata/Example_Old_Style_1.csv.xz
opm/inst/testdata/Example_Old_Style_2.csv.xz
opm/inst/testdata/Example_Old_Style_3.csv.xz
opm/inst/testdata/Example_Old_Style_Multiple.csv.xz
opm/inst/testdata/Example_Perkin_Elmer.txt.xz
opm/inst/testdata/Example_TECAN.txt.xz
opm/inst/tests
opm/inst/tests/test_aggregation-aux.R
opm/inst/tests/test_aggregation.R
opm/inst/tests/test_auxiliary-aux.R
opm/inst/tests/test_auxiliary.R
opm/inst/tests/test_classes-aux.R
opm/inst/tests/test_classes.R
opm/inst/tests/test_combination-aux.R
opm/inst/tests/test_combination.R
opm/inst/tests/test_constants.R
opm/inst/tests/test_conversion-aux.R
opm/inst/tests/test_conversion.R
opm/inst/tests/test_data.R
opm/inst/tests/test_dbio-aux.R
opm/inst/tests/test_dbio.R
opm/inst/tests/test_discretization.R
opm/inst/tests/test_getter.R
opm/inst/tests/test_imports.R
opm/inst/tests/test_io-aux.R
opm/inst/tests/test_io.R
opm/inst/tests/test_kmeans-aux.R
opm/inst/tests/test_kmeans.R
opm/inst/tests/test_metadata.R
opm/inst/tests/test_multcomp-aux.R
opm/inst/tests/test_multcomp.R
opm/inst/tests/test_naming-aux.R
opm/inst/tests/test_naming.R
opm/inst/tests/test_package.R
opm/inst/tests/test_phylogeny-aux.R
opm/inst/tests/test_phylogeny.R
opm/inst/tests/test_plate-map.R
opm/inst/tests/test_plotting-aux.R
opm/inst/tests/test_plotting.R
opm/inst/tests/test_splinefit-aux.R
opm/inst/tests/test_substrate-info.R
opm/inst/tests/test_testing-aux.R
opm/inst/tests/test_well-map.R
opm/man
opm/man/OPM.Rd
opm/man/OPM_DB.Rd
opm/man/WMD.Rd
opm/man/aggregated.Rd
opm/man/annotated.Rd
opm/man/as.data.frame.Rd
opm/man/batch_opm.Rd
opm/man/boccuto_et_al.Rd
opm/man/bracket.Rd
opm/man/bracket.set.Rd
opm/man/c.Rd
opm/man/ci_plot.Rd
opm/man/collect_template.Rd
opm/man/csv_data.Rd
opm/man/dim.Rd
opm/man/discrete.Rd
opm/man/discretized.Rd
opm/man/do_aggr.Rd
opm/man/do_disc.Rd
opm/man/duplicated.Rd
opm/man/explode_dir.Rd
opm/man/extract.Rd
opm/man/find_substrate.Rd
opm/man/has_aggr.Rd
opm/man/heat_map.Rd
opm/man/html_args.Rd
opm/man/include_metadata.Rd
opm/man/infix.k.Rd
opm/man/infix.q.Rd
opm/man/kmeans.Rd
opm/man/level_plot.Rd
opm/man/max.Rd
opm/man/measurements.Rd
opm/man/merge.Rd
opm/man/metadata.Rd
opm/man/metadata.set.Rd
opm/man/opm.package.Rd
opm/man/opm_dbput.Rd
opm/man/opm_files.Rd
opm/man/opm_mcp.Rd
opm/man/opm_opt.Rd
opm/man/opms.function.Rd
opm/man/opmx.function.Rd
opm/man/parallel_plot.Rd
opm/man/phylo_data.Rd
opm/man/plate_type.Rd
opm/man/plates.Rd
opm/man/potato.Rd
opm/man/radial_plot.Rd
opm/man/read_opm.Rd
opm/man/run_kmeans.Rd
opm/man/separate.Rd
opm/man/set_spline_options.Rd
opm/man/sort.Rd
opm/man/subset.Rd
opm/man/substrate_info.Rd
opm/man/summary.Rd
opm/man/to_yaml.Rd
opm/man/vaas_4.Rd
opm/man/wells.Rd
opm/man/xy_plot.Rd
opm/tests
opm/tests/run-all.R
opm/vignettes
opm/vignettes/opm-growth-curves.Rnw
opm/vignettes/opm-substrates.Rnw
opm/vignettes/opm-tutorial.Rnw