Analysing Phenotype Microarray and Growth Curve Data


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Documentation for package ‘opm’ version 1.3.63

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A B C D E F G H I K L M O P R S T U V W X Y misc

opm.package-package The 'opm' package

-- A --

aggregated Get aggregated data
aggregated-method Get aggregated data
aggregated-methods Get aggregated data
aggr_settings Get aggregated data
aggr_settings-method Get aggregated data
aggr_settings-methods Get aggregated data
annotated Create vector or matrix with substrate annotation
annotated-method Create vector or matrix with substrate annotation
annotated-methods Create vector or matrix with substrate annotation
anyDuplicated Determine duplicated plates
anyDuplicated-method Determine duplicated plates
anyDuplicated-methods Determine duplicated plates
anyNA Are aggregated or discretised data present?
anyNA-method Are aggregated or discretised data present?
anyNA-methods Are aggregated or discretised data present?
as.data.frame Create data frame
as.data.frame-method Create data frame
as.data.frame-methods Create data frame

-- B --

batch_collect Helper functions for file input and output
batch_opm Batch-convert PM data
batch_process Helper functions for file input and output
best_cutoff Discretisation functions
best_cutoff-method Discretisation functions
best_cutoff-methods Discretisation functions
boccuto_et_al Autism cell-line example data set
borders Work with k-means results
borders.Ckmeans.1d.dp Work with k-means results
borders.kmeans Work with k-means results
borders.kmeanss Work with k-means results
bracket-method Select subset
bracket-methods Select subset
bracket.set-method Assign subset
bracket.set-methods Assign subset

-- C --

c Combination and addition of plates
c-method Combination and addition of plates
c-methods Combination and addition of plates
calinski Work with k-means results
calinski.Ckmeans.1d.dp Work with k-means results
calinski.kmeans Work with k-means results
calinski.kmeanss Work with k-means results
ci_plot Plot point estimates with CIs
ci_plot-method Plot point estimates with CIs
ci_plot-methods Plot point estimates with CIs
collect_template Input metadata
collect_template-method Input metadata
collect_template-methods Input metadata
contains Determine duplicated plates
contains-method Determine duplicated plates
contains-methods Determine duplicated plates
csv_data Information from input CSV file
csv_data-method Information from input CSV file
csv_data-methods Information from input CSV file

-- D --

dim Get dimensions
dim-method Get dimensions
dim-methods Get dimensions
discrete Discretisation functions
discrete-method Discretisation functions
discrete-methods Discretisation functions
discretized Get discretised data
discretized-method Get discretised data
discretized-methods Get discretised data
disc_settings Get discretised data
disc_settings-method Get discretised data
disc_settings-methods Get discretised data
dollar.set-method Assign subset
dollar.set-methods Assign subset
double.bracket.set-method Assign subset
double.bracket.set-methods Assign subset
do_aggr Aggregate kinetics using curve-parameter estimation
do_aggr-method Aggregate kinetics using curve-parameter estimation
do_aggr-methods Aggregate kinetics using curve-parameter estimation
do_disc Discretise curve parameters
do_disc-method Discretise curve parameters
do_disc-methods Discretise curve parameters
duplicated Determine duplicated plates
duplicated-method Determine duplicated plates
duplicated-methods Determine duplicated plates

-- E --

edit Add or map metadata or edit them by hand
edit-method Add or map metadata or edit them by hand
edit-methods Add or map metadata or edit them by hand
explode_dir Helper functions for file input and output
extract Extract aggregated values and/or metadata
extract-method Extract aggregated values and/or metadata
extract-methods Extract aggregated values and/or metadata
extract_columns Extract aggregated values and/or metadata
extract_columns-method Extract aggregated values and/or metadata
extract_columns-methods Extract aggregated values and/or metadata

-- F --

file_pattern Helper functions for file input and output
find_positions Identify substrates or positions
find_positions-method Identify substrates or positions
find_positions-methods Identify substrates or positions
find_substrate Identify substrates or positions
find_substrate-method Identify substrates or positions
find_substrate-methods Identify substrates or positions
flatten Create data frame
flatten-method Create data frame
flatten-methods Create data frame
FOE Virtual classes of the 'opm' package
FOE-class Virtual classes of the 'opm' package

-- G --

gen_iii Plate type displayed or modified, registered or deleted
gen_iii-method Plate type displayed or modified, registered or deleted
gen_iii-methods Plate type displayed or modified, registered or deleted
glob_to_regex Helper functions for file input and output
glob_to_regex.character Helper functions for file input and output
glob_to_regex.factor Helper functions for file input and output

-- H --

has_aggr Are aggregated or discretised data present?
has_aggr-method Are aggregated or discretised data present?
has_aggr-methods Are aggregated or discretised data present?
has_disc Are aggregated or discretised data present?
has_disc-method Are aggregated or discretised data present?
has_disc-methods Are aggregated or discretised data present?
heat_map Heat map
heat_map-method Heat map
heat_map-methods Heat map
hist.Ckmeans.1d.dp Work with k-means results
hist.kmeans Work with k-means results
hist.kmeanss Work with k-means results
hours Stored measurements
hours-method Stored measurements
hours-methods Stored measurements
html_args HTML formatting and output label generation

-- I --

include_metadata Add or map metadata or edit them by hand
include_metadata-method Add or map metadata or edit them by hand
include_metadata-methods Add or map metadata or edit them by hand
infix.k Query metadata keys
infix.k-method Query metadata keys
infix.k-methods Query metadata keys
infix.largek Query metadata keys
infix.largek-method Query metadata keys
infix.largek-methods Query metadata keys
infix.largeq Query metadata
infix.largeq-method Query metadata
infix.largeq-methods Query metadata
infix.q Query metadata
infix.q-method Query metadata
infix.q-methods Query metadata

-- K --

kmeans Work with k-means results

-- L --

length-method Get dimensions
length-methods Get dimensions
level_plot Level plot
level_plot-method Level plot
level_plot-methods Level plot
listing Listing of well names
listing-method Listing of well names
listing-methods Listing of well names

-- M --

map_metadata Add or map metadata or edit them by hand
map_metadata-method Add or map metadata or edit them by hand
map_metadata-methods Add or map metadata or edit them by hand
map_values Add or map metadata or edit them by hand
map_values-method Add or map metadata or edit them by hand
map_values-methods Add or map metadata or edit them by hand
max Overall or minimal maximum
max-method Overall or minimal maximum
max-methods Overall or minimal maximum
measurements Stored measurements
measurements-method Stored measurements
measurements-methods Stored measurements
merge Merge or split plates
merge-method Merge or split plates
merge-methods Merge or split plates
metadata Get metadata
metadata-method Get metadata
metadata-methods Get metadata
metadata.set Replace metadata
metadata.set-method Replace metadata
metadata.set-methods Replace metadata
metadata<- Replace metadata
metadata<--method Replace metadata
metadata_chars Get metadata
metadata_chars-method Get metadata
metadata_chars-methods Get metadata
minmax Overall or minimal maximum
minmax-method Overall or minimal maximum
minmax-methods Overall or minimal maximum
MOPMX Real classes of the 'opm' package
MOPMX-class Real classes of the 'opm' package

-- O --

oapply Get available plates or apply function to them
oapply-method Get available plates or apply function to them
oapply-methods Get available plates or apply function to them
OPM Real classes of the 'opm' package
OPM-class Real classes of the 'opm' package
opm.package The 'opm' package
OPMA Real classes of the 'opm' package
OPMA-class Real classes of the 'opm' package
OPMA_DB Classes for 'opm' database I/O
OPMA_DB-class Classes for 'opm' database I/O
OPMD Real classes of the 'opm' package
OPMD-class Real classes of the 'opm' package
OPMD_DB Classes for 'opm' database I/O
OPMD_DB-class Classes for 'opm' database I/O
OPMS Real classes of the 'opm' package
opms OPMS constructor
OPMS-class Real classes of the 'opm' package
OPMX Virtual classes of the 'opm' package
opmx Convert user-defined objects to OPMX
OPMX-class Virtual classes of the 'opm' package
opmx-method Convert user-defined objects to OPMX
opmx-methods Convert user-defined objects to OPMX
OPM_DB Classes for 'opm' database I/O
OPM_DB-class Classes for 'opm' database I/O
opm_dbcheck Database I/O for 'opm'
opm_dbcheck-method Database I/O for 'opm'
opm_dbcheck-methods Database I/O for 'opm'
opm_dbclass Database I/O for 'opm'
opm_dbclass-method Database I/O for 'opm'
opm_dbclass-methods Database I/O for 'opm'
opm_dbclear Database I/O for 'opm'
opm_dbclear-method Database I/O for 'opm'
opm_dbclear-methods Database I/O for 'opm'
opm_dbfind Database I/O for 'opm'
opm_dbfind-method Database I/O for 'opm'
opm_dbfind-methods Database I/O for 'opm'
opm_dbget Database I/O for 'opm'
opm_dbget-method Database I/O for 'opm'
opm_dbget-methods Database I/O for 'opm'
opm_dbnext Database I/O for 'opm'
opm_dbnext-method Database I/O for 'opm'
opm_dbnext-methods Database I/O for 'opm'
opm_dbput Database I/O for 'opm'
opm_dbput-method Database I/O for 'opm'
opm_dbput-methods Database I/O for 'opm'
opm_files Files and colour sets used by the package
opm_mcp Multiple comparison of group means
opm_mcp-method Multiple comparison of group means
opm_mcp-methods Multiple comparison of group means
OPM_MCP_OUT Real classes of the 'opm' package
OPM_MCP_OUT-class Real classes of the 'opm' package
opm_opt Global 'opm' options
opm_opt-method Global 'opm' options
opm_opt-methods Global 'opm' options

-- P --

parallelplot Parallel plot
parallelplot-method Parallel plot
parallelplot-methods Parallel plot
parallel_plot Parallel plot
parallel_plot-method Parallel plot
parallel_plot-methods Parallel plot
param_names Global 'opm' options
param_names-method Global 'opm' options
param_names-methods Global 'opm' options
phylo_data Export phylogenetic data
phylo_data-method Export phylogenetic data
phylo_data-methods Export phylogenetic data
plates Get available plates or apply function to them
plates-method Get available plates or apply function to them
plates-methods Get available plates or apply function to them
plate_type Plate type displayed or modified, registered or deleted
plate_type-method Plate type displayed or modified, registered or deleted
plate_type-methods Plate type displayed or modified, registered or deleted
plot.kmeanss Work with k-means results
plus Combination and addition of plates
plus-method Combination and addition of plates
plus-methods Combination and addition of plates
potato Potato cell-line growth data set

-- R --

radial_plot Radial plot
radial_plot-method Radial plot
radial_plot-methods Radial plot
read_opm Read multiple PM files at once or read single PM file
read_single_opm Read multiple PM files at once or read single PM file
register_plate Plate type displayed or modified, registered or deleted
register_plate-method Plate type displayed or modified, registered or deleted
register_plate-methods Plate type displayed or modified, registered or deleted
rep Sort, unify, revert or repeat OPMS objects
rep-method Sort, unify, revert or repeat OPMS objects
rep-methods Sort, unify, revert or repeat OPMS objects
rev Sort, unify, revert or repeat OPMS objects
rev-method Sort, unify, revert or repeat OPMS objects
rev-methods Sort, unify, revert or repeat OPMS objects
run_kmeans Conduct k-means partitioning
run_kmeans-method Conduct k-means partitioning
run_kmeans-methods Conduct k-means partitioning

-- S --

safe_labels HTML formatting and output label generation
select_colors Files and colour sets used by the package
separate Regularly split character vectors if possible
separate-method Regularly split character vectors if possible
separate-methods Regularly split character vectors if possible
seq Get dimensions
seq-method Get dimensions
seq-methods Get dimensions
set_spline_options Spline options
show-method Summarise OPMX or MOPMX objects
show-methods Summarise OPMX or MOPMX objects
sort Sort, unify, revert or repeat OPMS objects
sort-method Sort, unify, revert or repeat OPMS objects
sort-methods Sort, unify, revert or repeat OPMS objects
split Merge or split plates
split-method Merge or split plates
split-methods Merge or split plates
split_files Helper functions for file input and output
str-method Summarise OPMX or MOPMX objects
str-methods Summarise OPMX or MOPMX objects
subset Select a subset of the plates (or time points)
subset-method Select a subset of the plates (or time points)
subset-methods Select a subset of the plates (or time points)
substrate_info Provide information on substrates
substrate_info-method Provide information on substrates
substrate_info-methods Provide information on substrates
summary Summarise OPMX or MOPMX objects
summary-method Summarise OPMX or MOPMX objects
summary-methods Summarise OPMX or MOPMX objects

-- T --

thin_out Select a subset of the plates (or time points)
thin_out-method Select a subset of the plates (or time points)
thin_out-methods Select a subset of the plates (or time points)
to_kmeans Work with k-means results
to_kmeans.Ckmeans.1d.dp Work with k-means results
to_kmeans.kmeans Work with k-means results
to_kmeans.kmeanss Work with k-means results
to_metadata Input metadata
to_metadata-method Input metadata
to_metadata-methods Input metadata
to_yaml Convert to YAML
to_yaml-method Convert to YAML
to_yaml-methods Convert to YAML

-- U --

unique Sort, unify, revert or repeat OPMS objects
unique-method Sort, unify, revert or repeat OPMS objects
unique-methods Sort, unify, revert or repeat OPMS objects

-- V --

vaas_1 Example data sets from Vaas et al. (2012)
vaas_4 Example data sets from Vaas et al. (2012)

-- W --

well Stored measurements
well-method Stored measurements
well-methods Stored measurements
wells Listing of well names
wells-method Listing of well names
wells-methods Listing of well names
WMD Virtual classes of the 'opm' package
WMD-class Virtual classes of the 'opm' package
WMDS Virtual classes of the 'opm' package
WMDS-class Virtual classes of the 'opm' package
WMDX Virtual classes of the 'opm' package
WMDX-class Virtual classes of the 'opm' package

-- X --

XOPMX Virtual classes of the 'opm' package
XOPMX-class Virtual classes of the 'opm' package
xy_plot X-Y plot
xy_plot-method X-Y plot
xy_plot-methods X-Y plot

-- Y --

YAML_VIA_LIST Virtual classes of the 'opm' package
YAML_VIA_LIST-class Virtual classes of the 'opm' package

-- misc --

$<- Assign subset
$<--method Assign subset
%K% Query metadata keys
%k% Query metadata keys
%K%-method Query metadata keys
%k%-method Query metadata keys
%Q% Query metadata
%q% Query metadata
%Q%-method Query metadata
%q%-method Query metadata
+-method Combination and addition of plates
[ Select subset
[-method Select subset
[<- Assign subset
[<--method Assign subset
[[<- Assign subset
[[<--method Assign subset