Description Usage Arguments Details Value References See Also Examples
Combine all plates in a single OPM
object
by treating them as originating from subsequent runs of
the same experimental plate. Adjust the times
accordingly. Alternatively, split plates according to the
contained regular series of substrates, if any. The
MOPMX
method merges according to plate
types, optionally including a novel element.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 | ## S4 method for signature 'CMAT,ANY'
merge(x, y)
## S4 method for signature 'CMAT,factor'
merge(x, y)
## S4 method for signature 'CMAT,logical'
merge(x, y)
## S4 method for signature 'MOPMX,ANY'
merge(x, y)
## S4 method for signature 'MOPMX,missing'
merge(x, y)
## S4 method for signature 'OPM,OPM'
merge(x, y, sort.first = TRUE, parse = TRUE)
## S4 method for signature 'OPM,missing'
merge(x, y, sort.first = TRUE, parse = TRUE)
## S4 method for signature 'OPM,numeric'
merge(x, y, sort.first = TRUE, parse = TRUE)
## S4 method for signature 'OPMS,missing'
merge(x, y, sort.first = TRUE, parse = TRUE)
## S4 method for signature 'OPMS,numeric'
merge(x, y, sort.first = TRUE, parse = TRUE)
## S4 method for signature 'MOPMX,ANY,ANY'
split(x, f, drop)
## S4 method for signature 'MOPMX,ANY,missing'
split(x, f, drop)
## S4 method for signature 'MOPMX,factor,ANY'
split(x, f, drop)
## S4 method for signature 'MOPMX,factor,missing'
split(x, f, drop)
## S4 method for signature 'MOPMX,list,ANY'
split(x, f, drop)
## S4 method for signature 'MOPMX,list,missing'
split(x, f, drop)
## S4 method for signature 'OPM,ANY,missing'
split(x, f, drop)
## S4 method for signature 'OPM,factor,ANY'
split(x, f, drop)
## S4 method for signature 'OPM,factor,missing'
split(x, f, drop)
## S4 method for signature 'OPM,missing,ANY'
split(x, f, drop)
## S4 method for signature 'OPM,missing,missing'
split(x, f, drop)
## S4 method for signature 'OPMS,ANY,missing'
split(x, f, drop)
## S4 method for signature 'OPMS,factor,ANY'
split(x, f, drop)
## S4 method for signature 'OPMS,factor,missing'
split(x, f, drop)
## S4 method for signature 'OPMS,missing,ANY'
split(x, f, drop)
## S4 method for signature 'OPMS,missing,missing'
split(x, f, drop)
## S4 method for signature 'OPMX,ANY,ANY'
split(x, f, drop)
|
x |
|
y |
For the If For the |
sort.first |
Logical scalar. Sort the plates according to their setup times before merging? |
parse |
Logical scalar. Ignored unless
|
f |
For the If a factor, If neither missing nor a factor, For the If |
drop |
Passed to |
This OPMS
method of merge
is
intended for dealing with slowly growing or reacting
organisms that need to be analysed with subsequent runs
of the same plate in PM mode. Results obtained
with Geodermatophilus strains and Generation-III
plates indicate that this works well in practice. See the
references, and see the documentation of the
montero_et_al
data set in the opmdata
package.
See the arguments time.fmt
and time.zone
of
opm_opt
for modifying the parsing of
setup-time entries. If it does not work, additional
time-string templates must be stored.
The CMAT
method of merge
is only for
internal use.
The split
methods with missing f
are for
splitting plates that contain series of substrate-usage
assays as indicated in the full substrate names (mostly
interpretable as concentrations). OPMS
objects are generated that contain each replicate within
the series in a separate plate and the replicate
ID indicated in the metadata entry given by
opm_opt("series.key")
. This allows for
comparisons between within-plate replicates.
Splitting according to substrate series will not work if
these are not regular, i.e. the same substrates occur in
each replicate. In such cases x
will be returned,
with a warning. Substrates without a replicate
(‘concentration’) indicator would silently be
skipped, however. The composition and order of the wells
per pseudo-plate must be made uniform. This is done by
enforcing well names and well ordering of the first
replicate in all forthcoming replicates.
After a successful splitting, the numeric suffixes in the
full well names make no sense any more, as each plate
contains a constant set of such suffixes. The
no.num
argument of wells
and the
dependent methods can be used to remove the suffixes
before displaying the full well names.
The MOPMX
method for merge
will
raise an error if elements occur within x
(and
optionally y
) that have the same plate type but
cannot be combined any way because they contain distinct
sets of wells. See the comments on combining plates into
a OPMS
object.
The OPMX
method of merge
yields an
OPM
object. The metadata
and
csv_data
will be taken from the first
contained plate, but aggregated values, if any, will be
dropped.
The MOPMX
method for merge
yields a
MOPMX
object with a potentially different
number of elements.
The split
methods yield either an
OPMS
or an MOPMX
object; the
MOPMX
method for split
yields a list
of MOPMX
objects.
Montero-Calasanz, M. d. C., Goeker, M., Poetter, G., Rohde, M., Sproeer, C., Schumann, P., Gorbushina, A. A., Klenk, H.-P. 2012 Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad. Extremophiles 16, 903–909.
Montero-Calasanz, M. d. C., Goeker, M., Rohde, M., Schumann, P., Poetter, G., Sproeer, C., Gorbushina, A. A., Klenk, H.-P. 2013 Geodermatophilus siccatus sp. nov., isolated from arid sand of the Saharan desert in Chad. Antonie van Leeuwenhoek 103, 449–456.
opmdata::montero_et_al
Other conversion-functions: as.data.frame
,
extract
, extract_columns
,
flatten
, oapply
,
opmx
, plates
,
rep
, rev
, sort
,
to_yaml
, unique
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ## merge: OPM methods
stopifnot(identical(merge(vaas_1, 0.5), vaas_1)) # nothing to merge
summary(x <- merge(vaas_1, vaas_1)) # biologically unreasonable!
stopifnot(is(x, "OPM"), dim(x) == c(2 * hours(vaas_1, "size"), 96))
## merge: OPMS methods
summary(x <- merge(vaas_4)) # biologically unreasonable for these data!
stopifnot(is(x, "OPM"), dim(x) == c(sum(hours(vaas_4, "size")), 96))
# See opmdata::montero_et_al for an object to which this can be sensibly
# applied. An according example is given in the montero_et_al documentation.
## split: OPM methods
(x <- split(vaas_1))
metadata(x, opm_opt("series.key"))
stopifnot(is(x, "OPMS"), dim(x) == c(2, hours(vaas_1, "size"), 1))
# only D-Serine is present as series, all other wells are skipped
# thus split is more useful when applied to other plate types such as "ECO"
(x <- split(vaas_1, "Species"))
stopifnot(is(x, "MOPMX"), length(x) == 1)
## split: OPMS methods
(x <- split(vaas_4))
metadata(x, opm_opt("series.key"))
stopifnot(is(x, "OPMS"), dim(x) == c(8, hours(vaas_4, "size")[1], 1))
(x <- split(vaas_4, "Species"))
stopifnot(is(x, "MOPMX"), length(x) == 2)
# Split into list of OPMS objects with the same overall measurement hours
x <- split(vaas_4, as.factor(hours(vaas_4)))
stopifnot(is(x, "MOPMX"), length(x) == 1, class(x[[1]]) == "OPMS")
# ... because the running times were actually already identical, the list
# contains only a single element.
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