| Title: | Functionality for Mass Spectrometry Features |
|---|---|
| Description: | The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages. |
| Authors: | Johannes Rainer [aut, cre] |
| Maintainer: | Johannes Rainer <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.13.0 |
| Built: | 2024-06-30 05:12:38 UTC |
| Source: | https://github.com/bioc/MsFeatures |
corRows is a simple function to perform a pairwise correlation between
rows of a numeric matrix by calling stats::cor() on the transposed
input matrix x.
corRows( x, y = NULL, use = "pairwise.complete.obs", method = c("pearson", "kendall", "spearman"), ... )corRows( x, y = NULL, use = "pairwise.complete.obs", method = c("pearson", "kendall", "spearman"), ... )
x |
|
y |
not supported (ignored). |
use |
see information for parameter |
method |
see information for parameter |
... |
additional parameters (ignored). |
matrix with correlation coefficients between rows in x.
Johannes Rainer
## Define a simple numeric matrix x <- rbind( c(12, 34, 231, 234, 9, 5, 7), c(900, 900, 800, 10, 12, 9, 4), c(25, 70, 400, 409, 15, 8, 4), c(12, 13, 14, 15, 16, 17, 18), c(14, 36, 240, 239, 12, 7, 8) ) corRows(x) corRows(x, method = "spearman")## Define a simple numeric matrix x <- rbind( c(12, 34, 231, 234, 9, 5, 7), c(900, 900, 800, 10, 12, 9, 4), c(25, 70, 400, 409, 15, 8, 4), c(12, 13, 14, 15, 16, 17, 18), c(14, 36, 240, 239, 12, 7, 8) ) corRows(x) corRows(x, method = "spearman")
featureGroups and featureGroups<- allow to extract or set the feature
definitions from the input object. The implementations for
SummarizedExperiment() get or set the content of a column named
"feature_group" in the object's rowData.
This method should be implemented for all other object for which a
groupFeatures() method is defined.
featureGroups(object, ...) featureGroups(object) <- value ## S4 method for signature 'SummarizedExperiment' featureGroups(object) ## S4 replacement method for signature 'SummarizedExperiment' featureGroups(object) <- valuefeatureGroups(object, ...) featureGroups(object) <- value ## S4 method for signature 'SummarizedExperiment' featureGroups(object) ## S4 replacement method for signature 'SummarizedExperiment' featureGroups(object) <- value
object |
the input object. In the |
... |
ignored. |
value |
the new value for the feature groups variable. |
a character with the group assignment of the features. Has to have
the same length as there are features in object.
Johannes Rainer
## Load the test SummarizedExperiment library(SummarizedExperiment) data(se) ## No column "feature_group" present in the object, this NA is returned featureGroups(se) ## Add a column "feature_group" to the `rowData` of the object rowData(se)$feature_group <- seq_len(nrow(rowData(se))) featureGroups(se)## Load the test SummarizedExperiment library(SummarizedExperiment) data(se) ## No column "feature_group" present in the object, this NA is returned featureGroups(se) ## Add a column "feature_group" to the `rowData` of the object rowData(se)$feature_group <- seq_len(nrow(rowData(se))) featureGroups(se)
Group values with a difference between them being smaller than a user
defined threshold. This function uses the groupSimilarityMatrix() function
to create groups with smallest differences between its members. Differences
between all members of one group are below the user defined threshold
maxDiff. This is a more stringent grouping than what groupConsecutive()
performs leading thus to smaller groups (with smaller differences between
its members).
groupClosest(x, maxDiff = 1)groupClosest(x, maxDiff = 1)
x |
|
maxDiff |
|
integer with the group assignment (values grouped together have
the same return value).
Johannes Rainer
Other grouping operations:
groupConsecutive(),
groupSimilarityMatrix()
x <- c(1.1, 1.9, 2.2) groupClosest(x) ## Although the difference between the 1st and 2nd element would be smaller ## than the threshold, they are not grouped because the difference between ## the 2nd and 3rd element is even smaller. The first element is also not ## put into the same group, because it has a difference > diffRt to the 3rd ## element. x <- c(1.1, 1.5, 1.7, 2.3, 2.7, 4.3, 4.4, 4.9, 5.2, 5.4, 5.8, 6, 7, 9, 9.5, 15) groupClosest(x)x <- c(1.1, 1.9, 2.2) groupClosest(x) ## Although the difference between the 1st and 2nd element would be smaller ## than the threshold, they are not grouped because the difference between ## the 2nd and 3rd element is even smaller. The first element is also not ## put into the same group, because it has a difference > diffRt to the 3rd ## element. x <- c(1.1, 1.5, 1.7, 2.3, 2.7, 4.3, 4.4, 4.9, 5.2, 5.4, 5.8, 6, 7, 9, 9.5, 15) groupClosest(x)
groupConsecutive groups sorted values in x for which the difference
is smaller than maxDiff. As a result, the mean difference between the
groups will always be larger than maxDiff, but difference between
individual values within the same group (e.g. between the first and last)
can be larger maxDiff.
In detail, from the sorted x, the function starts from the smallest value
defining the first group as the one containing all values in x with a
difference to this first value which is <= maxDiff.
The next group is the defined based on the next larger value that is not part
of the first group and includes all values with a difference <= maxDiff to
this value. For values fulfilling this criteria but being already part of
a previous group, the differences to the mean value of the current group
and to the mean of previous groups are compared and values are assigned to
the group to which they have the smallest difference.
Example: values 1.1, 1.9, 2.2 should be grouped with a maxDiff = 1. The
first group is defined to include all values for which the difference to the
first value (1.1) is smaller maxDiff. Thus, the first group is defined
to contain values 1.1 and 1.9. Then the next group is defined based on the
next larger value not part of any group, 2.2. This group contains values
1.9 and 2.2 with the value 1.9 being already assigned to the first
group. The difference between this value 1.9 and the mean of the
current group (mean(c(1.9, 2.2)) is then compared to the difference of
1.9 to the mean value of the group 1.9 is already part of
(which is mean(c(1.1, 1.9))). Since the difference to the second group is
smaller, 1.9 is removed from the first group and assigned to the second
one.
groupConsecutive(x, maxDiff = 1)groupConsecutive(x, maxDiff = 1)
x |
|
maxDiff |
|
integer with the group assignment (values grouped together have
the same return value).
The difference between consecutive (ordered) values within a defined group
is always <= maxDiff, but the difference between e.g. the first and the
last of the (ordered) values can be larger than maxDiff. See
groupClosest() for a more stringent grouping function.
Johannes Rainer
Other grouping operations:
groupClosest(),
groupSimilarityMatrix()
## The example described above x <- c(1.1, 1.9, 2.2) groupConsecutive(x) x <- c(1.1, 1.5, 1.7, 2.3, 2.7, 4.3, 4.4, 4.9, 5.2, 5.4, 5.8, 6, 7, 9, 9.5, 15) groupConsecutive(x) ## value 5.2 was initially grouped with 4.3 (because their difference is ## smaller 1, but then re-grouped together with 5.4 because the difference ## between 5.4 (the next value outside the group of 4.3) and 5.2 is smaller ## than its difference to the mean value of the group for value 4.3 ## Example for a case in which values are NOT grouped into the same group ## even if the difference between them is <= maxDiff a <- c(4.9, 5.2, 5.4) groupConsecutive(a, maxDiff = 0.3)## The example described above x <- c(1.1, 1.9, 2.2) groupConsecutive(x) x <- c(1.1, 1.5, 1.7, 2.3, 2.7, 4.3, 4.4, 4.9, 5.2, 5.4, 5.8, 6, 7, 9, 9.5, 15) groupConsecutive(x) ## value 5.2 was initially grouped with 4.3 (because their difference is ## smaller 1, but then re-grouped together with 5.4 because the difference ## between 5.4 (the next value outside the group of 4.3) and 5.2 is smaller ## than its difference to the mean value of the group for value 4.3 ## Example for a case in which values are NOT grouped into the same group ## even if the difference between them is <= maxDiff a <- c(4.9, 5.2, 5.4) groupConsecutive(a, maxDiff = 0.3)
This documentation describes the general concepts of feature grouping, which can be achieved by the different approaches described further below.
The main function for the stepwise feature grouping is groupFeatures. The
selection of the actual grouping algorithm (along with the definition of its
parameters) is done by passing the respective parameter object, along with
the object containing the input data and optional additional arguments,
to the groupFeatures method.
groupFeatures(object, param, ...)groupFeatures(object, param, ...)
object |
input data object on which (with which data) the feature grouping should be performed. |
param |
parameter object which type defines the selection of the grouping algorithm. |
... |
additional arguments to be passed to the grouping algorithm. |
Depending on the implementation and the input object. Generally the input object with grouping results added. See respective help pages for more information.
Each feature grouping algorithm can be applied individually as a single-step approach, e.g. by grouping features only on a single feature property, such as the retention time. Additional feature grouping approaches might also be implemented that consider combination of different MS feature properties in a single clustering process.
Stepwise feature grouping evaluates a single property of MS features (such
as their retention time or abundances) at a time to define the feature
groups. Each subsequent grouping step builds on the previous one by
eventually sub-grouping each feature group, if needed. Thus, feature groups
get refined in each step. As an example, grouping of features based on a
similar retention time would loosely group features from all compounds
eluting at about the same time from a e.g. liquid chromatography run. This
obviously would also group features representing ions from different
co-eluting compounds. Thus, calling groupFeatures on the previous feature
grouping result with a different parameter object would refine these
initial feature groups, splitting them based on another property of the
features (such as correlation of feature abundances across samples).
The advantage of the stepwise approach is that results can be evaluated after each grouping step and parameters adapted if needed. Also, it provides flexibility by allowing to change the order of grouping approaches, or skip individual steps if not suitable for the available data or the experimental setup.
The major disadvantage is that a wrong group assignment in one of the initial steps can not be corrected for in later steps.
Johannes Rainer
featureGroups() for the function to extract (defined) feature
groups from a result object.
## For examples please refer to the help pages of the `SimilarRtimeParam` or ## `AbundanceSimilarityParam` objects. NULL## For examples please refer to the help pages of the `SimilarRtimeParam` or ## `AbundanceSimilarityParam` objects. NULL
Group features based on similar abundances (i.e. feature values) across
samples. Parameter subset allows to define a sub set of samples on which
the similarity calculation should be performed. It might for example be
better to exclude QC samples from the analysis because feature values are
supposed to be constant in these samples.
The function first calculates a nxn similarity matrix with n being the
number of features and subsequently groups features for which the similarity
is higher than the user provided threshold. Parameter simFun allows
to specify the function to calculate the pairwise similarities on the feature
values (eventually transformed by the function specified with parameter
transform). simFun defaults to a function that uses cor to calculate
similarities between rows in object but any function that calculates
similarities between rows and that returns a (symmetric) numeric similarity
matrix can be used.
If object is a SummarizedExperiment(): if a column "feature_group" is
found in SummarizedExperiment::colData() feature groups defined in that
column are further sub-grouped with this method. See groupFeatures() for
the general concept of this feature grouping.
Parameter groupFun allows to specify the function to group the features
based on the similarity function. It defaults to groupSimilarityMatrix. See
groupSimilarityMatrix() for details.
Additional settings for the groupFun and simFun functions can be passed
to the parameter object with the ... in the AbundanceSimilarityParam
constructor function. Other additional parameters specific for the type
of object can be passed via ... in the groupFeatures call.
AbundanceSimilarityParam( threshold = 0.9, simFun = corRows, groupFun = groupSimilarityMatrix, subset = integer(), transform = identity, ... ) ## S4 method for signature 'matrix,AbundanceSimilarityParam' groupFeatures(object, param, ...) ## S4 method for signature 'SummarizedExperiment,AbundanceSimilarityParam' groupFeatures(object, param, i = 1L, ...)AbundanceSimilarityParam( threshold = 0.9, simFun = corRows, groupFun = groupSimilarityMatrix, subset = integer(), transform = identity, ... ) ## S4 method for signature 'matrix,AbundanceSimilarityParam' groupFeatures(object, param, ...) ## S4 method for signature 'SummarizedExperiment,AbundanceSimilarityParam' groupFeatures(object, param, i = 1L, ...)
threshold |
|
simFun |
|
groupFun |
|
subset |
|
transform |
|
... |
for |
object |
object containing the feature abundances on which features should be grouped. |
param |
|
i |
for |
for object being a SummarizedExperiment: a SummarizedExperiment
with the grouping results added to a column "feature_group" in the
object's rowData. For object being a matrix: an integer of length
equal to the number of rows with the group identifiers.
Johannes Rainer
groupFeatures() for the general concept of feature grouping.
featureGroups() for the function to extract defined feature
groups from a SummarizedExperiment.
Other feature grouping methods:
groupFeatures-similar-rtime
## Define a simple numeric matrix on which we want to group the rows x <- rbind( c(12, 34, 231, 234, 9, 5, 7), c(900, 900, 800, 10, 12, 9, 4), c(25, 70, 400, 409, 15, 8, 4), c(12, 13, 14, 15, 16, 17, 18), c(14, 36, 240, 239, 12, 7, 8), c(100, 103, 80, 2, 3, 1, 1) ) ## Group rows based on similarity calculated with Pearson's correlation ## on the actual data values (without transforming them). res <- groupFeatures(x, AbundanceSimilarityParam()) res ## Use Spearman's rho to correlate rows of the log2 transformed x matrix res <- groupFeatures(x, AbundanceSimilarityParam(method = "spearman", transform = log2)) res ## Perform the grouping on a SummarizedExperiment library(SummarizedExperiment) data(se) ## Group features based on log2 transformed feature values in the first ## assay of the SummarizedExperiment res <- groupFeatures(se, param = AbundanceSimilarityParam(threshold = 0.7, transform = log2)) featureGroups(res) ## Perform feature grouping only on a subset of rows/features: featureGroups(res) <- NA_character_ featureGroups(res)[40:80] <- "FG" res <- groupFeatures(res, AbundanceSimilarityParam(transform = log2)) featureGroups(res)## Define a simple numeric matrix on which we want to group the rows x <- rbind( c(12, 34, 231, 234, 9, 5, 7), c(900, 900, 800, 10, 12, 9, 4), c(25, 70, 400, 409, 15, 8, 4), c(12, 13, 14, 15, 16, 17, 18), c(14, 36, 240, 239, 12, 7, 8), c(100, 103, 80, 2, 3, 1, 1) ) ## Group rows based on similarity calculated with Pearson's correlation ## on the actual data values (without transforming them). res <- groupFeatures(x, AbundanceSimilarityParam()) res ## Use Spearman's rho to correlate rows of the log2 transformed x matrix res <- groupFeatures(x, AbundanceSimilarityParam(method = "spearman", transform = log2)) res ## Perform the grouping on a SummarizedExperiment library(SummarizedExperiment) data(se) ## Group features based on log2 transformed feature values in the first ## assay of the SummarizedExperiment res <- groupFeatures(se, param = AbundanceSimilarityParam(threshold = 0.7, transform = log2)) featureGroups(res) ## Perform feature grouping only on a subset of rows/features: featureGroups(res) <- NA_character_ featureGroups(res)[40:80] <- "FG" res <- groupFeatures(res, AbundanceSimilarityParam(transform = log2)) featureGroups(res)
Group features based on similar retention time. This method is supposed to be
used as an initial crude grouping of LC-MS features based on the median
retention time of all their chromatographic peaks. All features with a
difference in their retention time which is <= parameter diffRt of the
parameter object are grouped together.
If object is a SummarizedExperiment(): if a column "feature_group" is
found in SummarizedExperiment::colData() feature groups defined in that
column are further sub-grouped with this method. See groupFeatures() for
the general concept of this feature grouping.
Also, it might be required to specify the column in the object's rowData
containing the retention times with the rtime parameter (which defaults
to rtime = "rtime".
Parameter groupFun allows to specify the function that should be used for
the actual grouping. Two possible choices are:
groupFun = groupClosest (the default): this method creates groups
of features with smallest differences in retention times between the
individual group members. All differences between group members are
< diffRt (in contrast to the other grouping functions listed below).
See groupSimilarityMatrix() (which is used for the actual grouping on
pairwise retention time differences) for more details.
groupFun = groupConsecutive: the groupConsecutive() function
groups values together if their difference is smaller than diffRt. This
function iterates over the sorted retention times starting the grouping
from the lowest value.
If the difference of a feature to more than one group is smaller diffRt
it is assigned to the group to which its retention time is closest (most
similar) to the mean retention time of that group. This leads to smaller
group sizes. Be aware that with this grouping differences in retention
times between individual features within a group could still be larger
diffRt. See groupConsecutive() for details and examples.
groupFun = MsCoreUtils::group: this function consecutively groups
elements together if their difference in retention time is smaller than
diffRt. If two features are grouped into one group, also all other
features with a retention time within the defined window to any of the two
features are also included into the feature group. This grouping is
recursively expanded which can lead, depending on diffRt, to very large
feature groups spanning a large retention time window. See
MsCoreUtils::group() for details.
Other grouping functions might be added in future. Alternatively it is also possible to provide a custom function for the grouping operation.
SimilarRtimeParam(diffRt = 1, groupFun = groupClosest) ## S4 method for signature 'numeric,SimilarRtimeParam' groupFeatures(object, param, ...) ## S4 method for signature 'SummarizedExperiment,SimilarRtimeParam' groupFeatures(object, param, rtime = "rtime", ...)SimilarRtimeParam(diffRt = 1, groupFun = groupClosest) ## S4 method for signature 'numeric,SimilarRtimeParam' groupFeatures(object, param, ...) ## S4 method for signature 'SummarizedExperiment,SimilarRtimeParam' groupFeatures(object, param, rtime = "rtime", ...)
diffRt |
|
groupFun |
|
object |
input object that provides the retention times that should be
grouped. The |
param |
|
... |
additional parameters passed to the |
rtime |
for |
Depending on parameter object:
for object being a numeric: returns a factor defining the feature
groups.
for object being SummarizedExperiment: returns the input object with
the feature group definition added to a column "feature_group" in the
result object's rowData.
Johannes Rainer
groupFeatures() for the general concept of feature grouping.
featureGroups() for the function to extract defined feature
groups from a SummarizedExperiment.
Other feature grouping methods:
groupFeatures-similar-abundance
## Simple grouping of a numeric vector. ## ## Define a numeric vector that could represent retention times of features x <- c(2, 3, 4, 5, 10, 11, 12, 14, 15) ## Group the values using a `group` function. This will create larger ## groups. groupFeatures(x, param = SimilarRtimeParam(2, MsCoreUtils::group)) ## Group values using the default `groupClosest` function. This creates ## smaller groups in which all elements have a difference smaller than the ## defined `diffRt` with each other. groupFeatures(x, param = SimilarRtimeParam(2, groupClosest)) ## Grouping on a SummarizedExperiment ## ## load the test SummarizedExperiment object library(SummarizedExperiment) data(se) ## No feature groups defined yet featureGroups(se) ## Determine the column that contains retention times rowData(se) ## Column "rtmed" contains the (median) retention time for each feature ## Group features that are eluting within 10 seconds res <- groupFeatures(se, SimilarRtimeParam(10), rtime = "rtmed") featureGroups(res) ## Evaluating differences between retention times within each feature group rts <- split(rowData(res)$rtmed, featureGroups(res)) lapply(rts, function(z) abs(diff(z)) <= 10) ## One feature group ("FG.053") has elements with a difference larger 10: rts[["FG.053"]] abs(diff(rts[["FG.053"]])) ## But the difference between the **sorted** retention times is < 10: abs(diff(sort(rts[["FG.053"]]))) ## Feature grouping with pre-defined feature groups: groupFeatures will ## sub-group the pre-defined feature groups, features with the feature group ## being `NA` are skipped. Below we perform the feature grouping only on ## features 40 to 70 fgs <- rep(NA, nrow(rowData(se))) fgs[40:70] <- "FG" featureGroups(se) <- fgs res <- groupFeatures(se, SimilarRtimeParam(10), rtime = "rtmed") featureGroups(res)## Simple grouping of a numeric vector. ## ## Define a numeric vector that could represent retention times of features x <- c(2, 3, 4, 5, 10, 11, 12, 14, 15) ## Group the values using a `group` function. This will create larger ## groups. groupFeatures(x, param = SimilarRtimeParam(2, MsCoreUtils::group)) ## Group values using the default `groupClosest` function. This creates ## smaller groups in which all elements have a difference smaller than the ## defined `diffRt` with each other. groupFeatures(x, param = SimilarRtimeParam(2, groupClosest)) ## Grouping on a SummarizedExperiment ## ## load the test SummarizedExperiment object library(SummarizedExperiment) data(se) ## No feature groups defined yet featureGroups(se) ## Determine the column that contains retention times rowData(se) ## Column "rtmed" contains the (median) retention time for each feature ## Group features that are eluting within 10 seconds res <- groupFeatures(se, SimilarRtimeParam(10), rtime = "rtmed") featureGroups(res) ## Evaluating differences between retention times within each feature group rts <- split(rowData(res)$rtmed, featureGroups(res)) lapply(rts, function(z) abs(diff(z)) <= 10) ## One feature group ("FG.053") has elements with a difference larger 10: rts[["FG.053"]] abs(diff(rts[["FG.053"]])) ## But the difference between the **sorted** retention times is < 10: abs(diff(sort(rts[["FG.053"]]))) ## Feature grouping with pre-defined feature groups: groupFeatures will ## sub-group the pre-defined feature groups, features with the feature group ## being `NA` are skipped. Below we perform the feature grouping only on ## features 40 to 70 fgs <- rep(NA, nrow(rowData(se))) fgs[40:70] <- "FG" featureGroups(se) <- fgs res <- groupFeatures(se, SimilarRtimeParam(10), rtime = "rtmed") featureGroups(res)
This function groups elements (rows or columns) of a diagonal matrix, such as
a pairwise correlation matrix or similarity matrix, with a value >= threshold. This creates clusters of elements in which all elements have
a value >= threshold with any other element in that cluster. On a
correlation matrix (such as created with cor) it will generate small
clusters of highly correlated elements. Note however that single elements in
one cluster could also have a correlation >= threshold to another element
in another cluster. The average similarity to its own cluster will however
be higher to that of the other.
groupSimilarityMatrix(x, threshold = 0.9, full = TRUE, ...)groupSimilarityMatrix(x, threshold = 0.9, full = TRUE, ...)
x |
symmetrix |
threshold |
|
full |
|
... |
ignored. |
The algorithm is defined as follows:
all pairs of values in x which are >= threshold are identified and
sorted decreasingly.
starting with the pair with the highest correlation, groups are defined:
if none of the two is in a group, both are put into the same new group.
if one of the two is already in a group, the other is put into the same
group if all correlations of it to that group are >= threshold
(and are not NA).
if both are already in the same group nothing is done.
if both are in different groups: an element is put into the group of the
other if a) all correlations of it to members of the other's group
are not NA and >= threshold and b) the average correlation to the
other group is larger than the average correlation to its own group.
This ensures that groups are defined in which all elements have a correlation
>= threshold with each other and the correlation between members of the
same group is maximized.
integer same length than nrow(x), grouped elements (rows) defined
by the same value.
Johannes Rainer
Other grouping operations:
groupClosest(),
groupConsecutive()
x <- rbind( c(1, 0.9, 0.6, 0.8, 0.5), c(0.9, 1, 0.7, 0.92, 0.8), c(0.6, 0.7, 1, 0.91, 0.7), c(0.8, 0.92, 0.91, 1, 0.9), c(0.5, 0.8, 0.7, 0.9, 1) ) groupSimilarityMatrix(x, threshold = 0.9) groupSimilarityMatrix(x, threshold = 0.1) ## Add also a correlation between 3 and 2 x[2, 3] <- 0.9 x[3, 2] <- 0.9 x groupSimilarityMatrix(x, threshold = 0.9) ## Add a higher correlation between 4 and 5 x[4, 5] <- 0.99 x[5, 4] <- 0.99 x groupSimilarityMatrix(x, threshold = 0.9) ## Increase correlation between 2 and 3 x[2, 3] <- 0.92 x[3, 2] <- 0.92 x groupSimilarityMatrix(x, threshold = 0.9) ## Don't break previous cluster!x <- rbind( c(1, 0.9, 0.6, 0.8, 0.5), c(0.9, 1, 0.7, 0.92, 0.8), c(0.6, 0.7, 1, 0.91, 0.7), c(0.8, 0.92, 0.91, 1, 0.9), c(0.5, 0.8, 0.7, 0.9, 1) ) groupSimilarityMatrix(x, threshold = 0.9) groupSimilarityMatrix(x, threshold = 0.1) ## Add also a correlation between 3 and 2 x[2, 3] <- 0.9 x[3, 2] <- 0.9 x groupSimilarityMatrix(x, threshold = 0.9) ## Add a higher correlation between 4 and 5 x[4, 5] <- 0.99 x[5, 4] <- 0.99 x groupSimilarityMatrix(x, threshold = 0.9) ## Increase correlation between 2 and 3 x[2, 3] <- 0.92 x[3, 2] <- 0.92 x groupSimilarityMatrix(x, threshold = 0.9) ## Don't break previous cluster!
The se variable is a SummarizedExperiment() object representing the
results from a xcms-based pre-processing of an LC-MS untargeted
metabolomics data set. The raw data files are provided in the faahKO
package. The pre-processing of this data set is described in detail in
the xcms vignette of the xcms package. This object was created from the
XCMSnExp result object with the quantify method.
## Load the data data(se) library(SummarizedExperiment) ## Access row (feature) data rowData(se)## Load the data data(se) library(SummarizedExperiment) ## Access row (feature) data rowData(se)