OPM {opm} | R Documentation |
Classes whose members can be generated and manipulated by an opm user: OPM, OPMA, OPMD, OPMS and MOPMX.
OPM is an acronym for
‘OmniLog(R)
Phenotype Microarray’. This is the class for holding
single-plate
OmniLog(R)
phenotype microarray data without aggregated values, but
with information read from the original input
CSV files as well as an additional arbitrary
amount of arbitrarily organised metadata. Objects of this
class are usually created by inputting files with
read_single_opm
or read_opm
,
not with a call to new
or as
.
OPM inherits from WMD
and, hence,
has all its methods.
Regarding the coercion of this class to other classes
(see the as
method from the methods
package), consider the following:
Conversion of its child classes to this class is straightforward, see the examples below.
The
coercion of this class (and its child classes) to a list
(and vice versa) is only for expert users and relies on a
mapping between slot names and keys in the list, i.e. the
list must be appropriately named. For instance, this is
the mechanism when reading from and writing to
YAML, see to_yaml
.
Coercions to other data frames and matrices first coerce
the measurements
and then add the other
slots as attributes.
Methods such as
flatten
and extract
might be
way more appropriate for converting OPM
objects.
OPMA is an acronym for ‘OPM,
aggregated’. This is the class for holding single-plate
OmniLog(R)
phenotype microarray data together with aggregated
values. Objects of this class are usually created by
calling do_aggr
on an OPM object,
or by inputting files with read_single_opm
or read_opm
if these files already contain
aggregated data.
OPMA inherits from OPM and, hence, has all its methods.
OPMD is an acronym for ‘OPM,
discretised’. This is the class for holding single-plate
OmniLog(R)
phenotype microarray data together with aggregated
and discretised values. Objects of this class
are usually created by calling do_disc
on
an OPMA object, or by inputting files with
read_single_opm
or read_opm
if these files already contain discretised data.
OPMD inherits from OPMA and, hence, has all its methods.
The discretised data are considered as
‘consistent’ with the curve parameter from which
they have been estimated if no FALSE
value
corresponds to curve parameter larger than the curve
parameter of any TRUE
value; NA
values are
not considered when checking consistency. The
strict.OPMD
entry of opm_opt
determines whether an error or only a warning is issued
in the case of inconsistency.
OPMS is the class for holding multiple-plate
OmniLog(R)
phenotype microarray data with or without aggregated or
discretised values. Regarding the name: OPMS is
just the plural of OPM. Objects of this class
are usually created by calling opms
or
other combination functions on OPM or derived
objects, or by inputting files with
read_opm
if these files altogether contain
more than a single plate. OPMS objects are not
normally created with a call to new
or as
.
The data may have been obtained from distinct organisms
and/or replicates, but must correspond to the
same plate type and must contain the same wells.
OPMS inherits from WMDS
and,
hence, has all its methods. As a rule, OPMS has
the same methods as the OPM class, but adapted
to a collection of more than one OPM object.
Also, OPMS can hold OPMD and
OPMA as well as OPM objects, even
though this is not indicated for all its methods in this
manual.
MOPMX is an object for holding OPMX
objects with potentially multiple plate types. Regarding
the name: the M stands for ‘multiple’.
MOPMX objects are generated by
read_opm(convert = "grp")
and
opms(group = TRUE)
. MOPMX objects
can also be created with new
or as
and then
further manipulated; see the examples below.
MOPMX objects in many aspects behave like
lists.
OPM_MCP_OUT is a data-frame based class useful
as intermediate result of opm_mcp
. See
there and its annotated
method for usages.
methods::Methods methods::new
Other classes: FOE
, OPMA_DB
,
OPMD_DB
, OPMX
,
OPM_DB
, WMD
,
WMDS
, WMDX
,
XOPMX
, YAML_VIA_LIST
## overview on the classes
showClass("OPM")
## Class "OPM" [package "opm"]
##
## Slots:
##
## Name: measurements csv_data metadata
## Class: matrix character list
##
## Extends:
## Class "WMD", directly
## Class "OPMX", directly
## Class "XOPMX", directly
## Class "YAML_VIA_LIST", directly
## Class "WMDX", by class "WMD", distance 2
##
## Known Subclasses:
## Class "OPMA", directly
## Class "OPMD", by class "OPMA", distance 2
showClass("OPMA")
## Class "OPMA" [package "opm"]
##
## Slots:
##
## Name: aggregated aggr_settings measurements csv_data
## Class: matrix list matrix character
##
## Name: metadata
## Class: list
##
## Extends:
## Class "OPM", directly
## Class "WMD", by class "OPM", distance 2
## Class "WMDX", by class "OPM", distance 3
## Class "OPMX", by class "OPM", distance 2
## Class "XOPMX", by class "OPM", distance 2
## Class "YAML_VIA_LIST", by class "OPM", distance 2
##
## Known Subclasses: "OPMD"
showClass("OPMD")
## Class "OPMD" [package "opm"]
##
## Slots:
##
## Name: discretized disc_settings aggregated aggr_settings
## Class: logical list matrix list
##
## Name: measurements csv_data metadata
## Class: matrix character list
##
## Extends:
## Class "OPMA", directly
## Class "OPM", by class "OPMA", distance 2
## Class "WMD", by class "OPMA", distance 3
## Class "WMDX", by class "OPMA", distance 4
## Class "OPMX", by class "OPM", distance 3
## Class "XOPMX", by class "OPM", distance 3
## Class "YAML_VIA_LIST", by class "OPM", distance 3
showClass("OPMS")
## Class "OPMS" [package "opm"]
##
## Slots:
##
## Name: plates
## Class: list
##
## Extends:
## Class "WMDS", directly
## Class "OPMX", directly
## Class "XOPMX", directly
## Class "YAML_VIA_LIST", directly
## Class "WMDX", by class "WMDS", distance 2
showClass("MOPMX")
## Class "MOPMX" [package "opm"]
##
## Slots:
##
## Name: .Data names
## Class: list character
##
## Extends:
## Class "list", from data part
## Class "XOPMX", directly
## Class "vector", by class "list", distance 2
## OPMX conversions with as()
showMethods("coerce", classes = c("OPM", "OPMA", "OPMD", "OPMS"))
## Function: coerce (package methods)
## from="OPM", to="OPMA"
## from="OPM", to="OPMD"
## from="OPM", to="OPM_DB"
## from="OPM", to="data.frame"
## from="OPM", to="list"
## from="OPM", to="matrix"
## from="OPMA", to="OPM"
## from="OPMA", to="OPMA_DB"
## from="OPMA", to="OPMD"
## from="OPMA", to="data.frame"
## from="OPMA", to="list"
## from="OPMA", to="matrix"
## from="OPMA_DB", to="OPMA"
## from="OPMA_DB", to="OPMS"
## from="OPMD", to="OPM"
## from="OPMD", to="OPMA"
## from="OPMD", to="OPMD_DB"
## from="OPMD", to="data.frame"
## from="OPMD", to="list"
## from="OPMD", to="matrix"
## from="OPMD_DB", to="OPMD"
## from="OPMD_DB", to="OPMS"
## from="OPMS", to="MOPMX"
## (inherited from: from="OPMX", to="MOPMX")
## from="OPMS", to="OPMA_DB"
## from="OPMS", to="OPMD_DB"
## from="OPMS", to="OPM_DB"
## from="OPMS", to="list"
## from="OPM_DB", to="OPM"
## from="OPM_DB", to="OPMS"
## from="list", to="OPM"
## from="list", to="OPMA"
## from="list", to="OPMD"
## from="list", to="OPMS"
data(vaas_1)
data(vaas_4)
(x <- as(vaas_1, "OPMA")) # drops the discretised data
## Class OPMA
## From file ./E. coli DSM
## 30083T_vim10_7B__1_28_PMX_0_8#30#2010_F_
## 7B_5.csv
## Hours measured 95.75
## Number of wells 96
## Plate type Gen III
## Position 7-B
## Setup time 8/30/2010 1:53:08 PM
## Metadata 5
## Aggregated TRUE
## Discretized FALSE
stopifnot(has_disc(vaas_1), !has_disc(x))
(x <- as(vaas_1, "OPM")) # drops the aggregated data
## Class OPM
## From file ./E. coli DSM
## 30083T_vim10_7B__1_28_PMX_0_8#30#2010_F_
## 7B_5.csv
## Hours measured 95.75
## Number of wells 96
## Plate type Gen III
## Position 7-B
## Setup time 8/30/2010 1:53:08 PM
## Metadata 5
## Aggregated FALSE
## Discretized FALSE
stopifnot(has_aggr(vaas_1), !has_aggr(x))
## MOPMX creation and conversion
(x <- new("MOPMX")) # don't do this with the other classes
## [1] Length Plate.type Aggregated Discretized
## <0 rows> (or 0-length row.names)
##
## => MOPMX object with 0 element(s), details are shown above.
## Access the elements with [[ or $ to apply specific methods.
(x <- as(vaas_1, "MOPMX"))
## Length Plate.type Aggregated Discretized
## Gen.III 1 Gen III TRUE TRUE
##
## => MOPMX object with 1 element(s), details are shown above.
## Access the elements with [[ or $ to apply specific methods.
(x <- as(vaas_4, "MOPMX"))
## Length Plate.type Aggregated Discretized
## Gen.III 4 Gen III 4 4
##
## => MOPMX object with 1 element(s), details are shown above.
## Access the elements with [[ or $ to apply specific methods.
# conversion backwards is only possible as long as the MOPMX object contains
# only a single OPMX object
showMethods("coerce", classes = "MOPMX")
## Function: coerce (package methods)
## from="MOPMX", to="OPMA_DB"
## from="MOPMX", to="OPMD_DB"
## from="MOPMX", to="OPMX"
## from="MOPMX", to="OPM_DB"
## from="OPMD", to="MOPMX"
## (inherited from: from="OPMX", to="MOPMX")
## from="OPMS", to="MOPMX"
## (inherited from: from="OPMX", to="MOPMX")
## from="OPMX", to="MOPMX"
## from="OPM_DB", to="MOPMX"
## from="list", to="MOPMX"