netCompare: Group Comparison of Network Properties
In stefpeschel/NetCoMi: Network Construction and Comparison for Microbiome Data
netCompare R Documentation
Group Comparison of Network Properties
Description
Calculate and compare network properties for microbial networks
using Jaccard's index, the Rand index, the Graphlet Correlation Distance,
and permutation tests.
Usage
netCompare(
x,
permTest = FALSE,
jaccQuant = 0.75,
lnormFit = NULL,
testRand = TRUE,
nPermRand = 1000L,
gcd = TRUE,
gcdOrb = c(0, 2, 5, 7, 8, 10, 11, 6, 9, 4, 1),
verbose = TRUE,
nPerm = 1000L,
adjust = "adaptBH",
trueNullMethod = "convest",
cores = 1L,
logFile = NULL,
seed = NULL,
fileLoadAssoPerm = NULL,
fileLoadCountsPerm = NULL,
storeAssoPerm = FALSE,
fileStoreAssoPerm = "assoPerm",
storeCountsPerm = FALSE,
fileStoreCountsPerm = c("countsPerm1", "countsPerm2"),
returnPermProps = FALSE,
returnPermCentr = FALSE,
assoPerm = NULL,
dissPerm = NULL
)
Arguments
x
object of class microNetProps (returned by
netAnalyze).
permTest
logical. If TRUE, a permutation test is conducted
to test centrality measures and global network properties for group
differences. Defaults to FALSE. May lead to a considerably increased
execution time!
jaccQuant
numeric value between 0 and 1 specifying the quantile
used as threshold to identify the most central nodes for each centrality
measure. The resulting sets of nodes are used to calculate Jaccard's index
(see details). Default is 0.75.
lnormFit
logical indicating whether a log-normal distribution should
be fitted to the calculated centrality values for determining Jaccard's
index (see details). If NULL (default), the value is adopted
from the input, i.e., equals the method used for determining hub nodes.
testRand
logical. If TRUE, a permutation test is conducted
for the adjusted Rand index (with H0: ARI = 0). Execution time may be
increased for large networks.
nPermRand
integer giving the number of permutations used for testing
the adjusted Rand index for being significantly different from zero.
Ignored if testRand = FALSE. Defaults to 1000L.
gcd
logical. If TRUE (default), the Graphlet Correlation
Distance (GCD) is computed.
gcdOrb
numeric vector with integers from 0 to 14 defining the orbits
used for calculating the GCD. Minimum length is 2.
Defaults to c(0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11),
thus excluding redundant orbits such as the orbit o3.
verbose
logical. If TRUE (default), status messages are shown.
nPerm
integer giving the number of permutations if
permTest = TRUE. Default is 1000L.
adjust
character indicating the method used for multiple testing
adjustment of the permutation p-values. Possible values are "lfdr"
(default) for local false discovery rate correction (via
fdrtool), "adaptBH" for the adaptive
Benjamini-Hochberg method (Benjamini and Hochberg, 2000), or one of
the methods provided by p.adjust (see
p.adjust.methods()).
trueNullMethod
character indicating the method used for estimating the
proportion of true null hypotheses from a vector of p-values. Used for the
adaptive Benjamini-Hochberg method for multiple testing adjustment (chosen
by adjust = "adaptBH"). Accepts the provided options of the
method argument of propTrueNull:
"convest"(default), "lfdr", "mean", and "hist".
Can alternatively be "farco" for the "iterative plug-in method"
proposed by Farcomeni (2007).
cores
integer indicating the number of CPU cores used for
permutation tests. If cores > 1, the tests are performed in parallel.
Is limited to the number of available CPU cores determined by
detectCores. Defaults to 1L (no parallelization).
logFile
character string naming the log file to which the current
iteration number is written (if permutation tests are performed). Defaults
to NULL so that no log file is generated.
seed
integer giving a seed for reproducibility of the results.
fileLoadAssoPerm
character giving the name or path (without file
extension) of the file containing the "permuted" association/dissimilarity
matrices that was generated by setting storeAssoPerm to
TRUE. Only used for permutation tests. If NULL, no
existing associations are used.
fileLoadCountsPerm
character giving the name or path (without file
extension) of the file containing the "permuted" count matrices that was
generated by setting storeCountsPerm to TRUE.
Only used for permutation tests, and if fileLoadAssoPerm = NULL.
If NULL, no existing count matrices are used.
storeAssoPerm
logical indicating whether the association/dissimilarity
matrices for the permuted data should be saved to a file.
The file name is given via fileStoreAssoPerm. If TRUE,
the computed "permutation" association/dissimilarity matrices can be reused
via fileLoadAssoPerm to save runtime. Defaults to FALSE.
Ignored if fileLoadAssoPerm is not NULL.
fileStoreAssoPerm
character giving the name of a file to which the
matrix with associations/dissimilarities of the permuted data is saved.
Can also be a path.
storeCountsPerm
logical indicating whether the permuted count matrices
should be saved to an external file. Defaults to FALSE.
Ignored if fileLoadCountsPerm is not NULL.
fileStoreCountsPerm
character vector with two elements giving the
names of two files storing the permuted count matrices belonging to the
two groups.
returnPermProps
logical. If TRUE, the global properties and
their absolute differences for the permuted data are returned.
returnPermCentr
logical. If TRUE, the centralities and
their absolute differences for the permuted data are returned.
assoPerm
only needed for output generated with NetCoMi v1.0.1! A list
with two elements used for the permutation procedure.
Each entry must contain association matrices for "nPerm"
permutations. This can be the "assoPerm" value as part of the
output either returned by diffnet or netCompare.
dissPerm
only needed for output generated with NetCoMi v1.0.1!
Usage analog to assoPerm if a dissimilarity measure has been used
for network construction.
Details
Permutation procedure:
Used for testing centrality measures and global network properties for
group differences.
The null hypothesis of the tests is defined as
H_0: c1_i - c2_i = 0,
where c1_i and
c2_i denote the centrality values of taxon i in group 1 and 2,
respectively.
To generate a sampling distribution of the differences under H_0,
the group labels are randomly reassigned to the samples while the group
sizes are kept. The associations are then re-estimated for each permuted
data set. The p-values are calculated as the proportion of
"permutation-differences" being larger than or equal to the observed
difference. In non-exact tests, a pseudo-count is added to the numerator
and denominator to avoid p-values of zero. Several methods for adjusting
the p-values for multiplicity are available.
Jaccard's index:
Jaccard's index expresses for each centrality measure how equal the sets of
most central nodes are among the two networks.
These sets are defined as nodes with a centrality value above a defined
quantile (via jaccQuant) either of the empirical distribution of the
centrality values (lnormFit = FALSE) or of a fitted log-normal
distribution (lnormFit = TRUE).
The index ranges from 0 to 1, where 1 means the sets of most central nodes
are exactly equal in both networks and 0 indicates that the
most central nodes are completely different.
The index is calculated as suggested by Real and Vargas (1996).
Rand index:
The Rand index is used to express whether the determined clusterings are
equal in both groups. The adjusted Rand index (ARI) ranges from -1 to 1,
where 1 indicates that the two clusterings are exactly equal. The expected
index value for two random clusterings is 0. The implemented test procedure
is in accordance with the explanations in Qannari et al. (2014),
where a p-value below the alpha levels means that ARI is significantly
higher than expected for two random clusterings.
Graphlet Correlation Distance:
A graphlet-based distance measure, which is defined as the Euclidean
distance of the upper triangle values of the Graphlet Correlation
Matrices (GCM) of two networks (Yaveroglu et al., 2014).
The GCM of a network is a matrix with Spearman's correlations between the
network's node orbits (Hocevar and Demsar, 2016).
See calcGCD for details.
Value
Object of class microNetComp with the following
elements:
jaccDeg,jaccBetw,jaccClose,jaccEigen Values of Jaccard's index
for the centrality measures
jaccHub Jaccard index for the sets of hub nodes
randInd Adjusted Rand index
randIndLCC Adjusted Rand index for the largest connected
component (LCC)
gcd Graphlet Correlation Distance (object of class gcd
returned by calcGCD)
gcdLCC Graphlet Correlation Distance for the LCC
properties List with calculated network properties
propertiesLCC List with calculated network properties of the
LCC
diffGlobal Vectors with differences of global properties
diffGlobalLCC Vectors with differences of global properties for
the LCC
diffCent Vectors with differences of the centrality values
countMatrices The two count matrices returned
by netConstruct
assoMatrices The two association matrices returned
by netConstruct
dissMatrices The two dissimilarity matrices returned
by netConstruct
adjaMatrices The two adjacency matrices returned
by netConstruct
groups Group names returned by netConstruct
paramsProperties Parameters used for network analysis
Additional output if permutation tests are conducted:
pvalDiffGlobal P-values of the tests for differential global
properties
pvalDiffGlobalLCC P-values of the tests for differential
global properties in the LCC
pvalDiffCentr P-values of the tests for differential centrality
values
pvalDiffCentrAdjust Adjusted p-values of the tests for
differential centrality values
permDiffGlobal nPerm x 10 matrix containing the absolute
differences of the ten global network properties (computed for the whole
network) for all nPerm permutations
permDiffGlobalLCC nPerm x 11 matrix containing the
absolute differences of the eleven global network properties (computed for
the LCC) for all nPerm permutations
permDiffCentr List with absolute differences of the four
centrality measures for all nPerm permutations. Each list contains
a nPerm x nNodes matrix.
References
\insertRefbenjamini2000adaptiveNetCoMi
\insertReffarcomeni2007someNetCoMi
\insertRefgill2010statisticalNetCoMi
\insertRefhocevar2016computationNetCoMi
\insertRefqannari2014significanceNetCoMi
\insertRefreal1996probabilisticNetCoMi
\insertRefyaveroglu2014revealingNetCoMi
See Also
summary.microNetComp, netConstruct,
netAnalyze
Examples
# Load data sets from American Gut Project (from SpiecEasi package)
data("amgut2.filt.phy")
# Split data into two groups: with and without seasonal allergies
amgut_season_yes <- phyloseq::subset_samples(amgut2.filt.phy,
SEASONAL_ALLERGIES == "yes")
amgut_season_no <- phyloseq::subset_samples(amgut2.filt.phy,
SEASONAL_ALLERGIES == "no")
amgut_season_yes
amgut_season_no
# Filter the 121 samples (sample size of the smaller group) with highest
# frequency to make the sample sizes equal and thus ensure comparability.
n_yes <- phyloseq::nsamples(amgut_season_yes)
# Network construction
amgut_net <- netConstruct(data = amgut_season_yes,
data2 = amgut_season_no,
measure = "pearson",
filtSamp = "highestFreq",
filtSampPar = list(highestFreq = n_yes),
filtTax = "highestVar",
filtTaxPar = list(highestVar = 30),
zeroMethod = "pseudoZO", normMethod = "clr")
# Network analysis
# Note: Please zoom into the GCM plot or open a new window using:
# x11(width = 10, height = 10)
amgut_props <- netAnalyze(amgut_net, clustMethod = "cluster_fast_greedy")
# Network plot
plot(amgut_props,
sameLayout = TRUE,
title1 = "Seasonal allergies",
title2 = "No seasonal allergies")
#--------------------------
# Network comparison
# Without permutation tests
amgut_comp1 <- netCompare(amgut_props, permTest = FALSE)
summary(amgut_comp1)
# With permutation tests (with only 100 permutations to decrease runtime)
amgut_comp2 <- netCompare(amgut_props,
permTest = TRUE,
nPerm = 100L,
cores = 1L,
storeCountsPerm = TRUE,
fileStoreCountsPerm = c("countsPerm1",
"countsPerm2"),
storeAssoPerm = TRUE,
fileStoreAssoPerm = "assoPerm",
seed = 123456)
# Rerun with a different adjustment method ...
# ... using the stored permutation count matrices
amgut_comp3 <- netCompare(amgut_props, adjust = "BH",
permTest = TRUE, nPerm = 100L,
fileLoadCountsPerm = c("countsPerm1",
"countsPerm2"),
seed = 123456)
# ... using the stored permutation association matrices
amgut_comp4 <- netCompare(amgut_props, adjust = "BH",
permTest = TRUE, nPerm = 100L,
fileLoadAssoPerm = "assoPerm",
seed = 123456)
# amgut_comp3 and amgut_comp4 should be equal
all.equal(amgut_comp3$adjaMatrices, amgut_comp4$adjaMatrices)
all.equal(amgut_comp3$properties, amgut_comp4$properties)
summary(amgut_comp2)
summary(amgut_comp3)
summary(amgut_comp4)
#--------------------------
# Use 'createAssoPerm' to create "permuted" count and association matrices
createAssoPerm(amgut_props, nPerm = 100,
computeAsso = TRUE,
fileStoreAssoPerm = "assoPerm",
storeCountsPerm = TRUE,
fileStoreCountsPerm = c("countsPerm1", "countsPerm2"),
append = FALSE, seed = 123456)
amgut_comp5 <- netCompare(amgut_props, permTest = TRUE, nPerm = 100L,
fileLoadAssoPerm = "assoPerm")
all.equal(amgut_comp3$properties, amgut_comp5$properties)
summary(amgut_comp5)
stefpeschel/NetCoMi documentation built on Feb. 4, 2024, 8:20 a.m.
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| netCompare | R Documentation |
Group Comparison of Network Properties
Description
Calculate and compare network properties for microbial networks using Jaccard's index, the Rand index, the Graphlet Correlation Distance, and permutation tests.
Usage
netCompare(
x,
permTest = FALSE,
jaccQuant = 0.75,
lnormFit = NULL,
testRand = TRUE,
nPermRand = 1000L,
gcd = TRUE,
gcdOrb = c(0, 2, 5, 7, 8, 10, 11, 6, 9, 4, 1),
verbose = TRUE,
nPerm = 1000L,
adjust = "adaptBH",
trueNullMethod = "convest",
cores = 1L,
logFile = NULL,
seed = NULL,
fileLoadAssoPerm = NULL,
fileLoadCountsPerm = NULL,
storeAssoPerm = FALSE,
fileStoreAssoPerm = "assoPerm",
storeCountsPerm = FALSE,
fileStoreCountsPerm = c("countsPerm1", "countsPerm2"),
returnPermProps = FALSE,
returnPermCentr = FALSE,
assoPerm = NULL,
dissPerm = NULL
)
Arguments
x |
object of class |
permTest |
logical. If |
jaccQuant |
numeric value between 0 and 1 specifying the quantile used as threshold to identify the most central nodes for each centrality measure. The resulting sets of nodes are used to calculate Jaccard's index (see details). Default is 0.75. |
lnormFit |
logical indicating whether a log-normal distribution should
be fitted to the calculated centrality values for determining Jaccard's
index (see details). If |
testRand |
logical. If |
nPermRand |
integer giving the number of permutations used for testing
the adjusted Rand index for being significantly different from zero.
Ignored if |
gcd |
logical. If |
gcdOrb |
numeric vector with integers from 0 to 14 defining the orbits used for calculating the GCD. Minimum length is 2. Defaults to c(0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11), thus excluding redundant orbits such as the orbit o3. |
verbose |
logical. If |
nPerm |
integer giving the number of permutations if
|
adjust |
character indicating the method used for multiple testing
adjustment of the permutation p-values. Possible values are |
trueNullMethod |
character indicating the method used for estimating the
proportion of true null hypotheses from a vector of p-values. Used for the
adaptive Benjamini-Hochberg method for multiple testing adjustment (chosen
by |
cores |
integer indicating the number of CPU cores used for
permutation tests. If cores > 1, the tests are performed in parallel.
Is limited to the number of available CPU cores determined by
|
logFile |
character string naming the log file to which the current
iteration number is written (if permutation tests are performed). Defaults
to |
seed |
integer giving a seed for reproducibility of the results. |
fileLoadAssoPerm |
character giving the name or path (without file
extension) of the file containing the "permuted" association/dissimilarity
matrices that was generated by setting |
fileLoadCountsPerm |
character giving the name or path (without file
extension) of the file containing the "permuted" count matrices that was
generated by setting |
storeAssoPerm |
logical indicating whether the association/dissimilarity
matrices for the permuted data should be saved to a file.
The file name is given via |
fileStoreAssoPerm |
character giving the name of a file to which the matrix with associations/dissimilarities of the permuted data is saved. Can also be a path. |
storeCountsPerm |
logical indicating whether the permuted count matrices
should be saved to an external file. Defaults to |
fileStoreCountsPerm |
character vector with two elements giving the names of two files storing the permuted count matrices belonging to the two groups. |
returnPermProps |
logical. If |
returnPermCentr |
logical. If |
assoPerm |
only needed for output generated with NetCoMi v1.0.1! A list
with two elements used for the permutation procedure.
Each entry must contain association matrices for |
dissPerm |
only needed for output generated with NetCoMi v1.0.1!
Usage analog to |
Details
Permutation procedure:
Used for testing centrality measures and global network properties for
group differences.
The null hypothesis of the tests is defined as
H_0: c1_i - c2_i = 0,
where c1_i and
c2_i denote the centrality values of taxon i in group 1 and 2,
respectively.
To generate a sampling distribution of the differences under H_0,
the group labels are randomly reassigned to the samples while the group
sizes are kept. The associations are then re-estimated for each permuted
data set. The p-values are calculated as the proportion of
"permutation-differences" being larger than or equal to the observed
difference. In non-exact tests, a pseudo-count is added to the numerator
and denominator to avoid p-values of zero. Several methods for adjusting
the p-values for multiplicity are available.
Jaccard's index:
Jaccard's index expresses for each centrality measure how equal the sets of
most central nodes are among the two networks.
These sets are defined as nodes with a centrality value above a defined
quantile (via jaccQuant) either of the empirical distribution of the
centrality values (lnormFit = FALSE) or of a fitted log-normal
distribution (lnormFit = TRUE).
The index ranges from 0 to 1, where 1 means the sets of most central nodes
are exactly equal in both networks and 0 indicates that the
most central nodes are completely different.
The index is calculated as suggested by Real and Vargas (1996).
Rand index:
The Rand index is used to express whether the determined clusterings are
equal in both groups. The adjusted Rand index (ARI) ranges from -1 to 1,
where 1 indicates that the two clusterings are exactly equal. The expected
index value for two random clusterings is 0. The implemented test procedure
is in accordance with the explanations in Qannari et al. (2014),
where a p-value below the alpha levels means that ARI is significantly
higher than expected for two random clusterings.
Graphlet Correlation Distance:
A graphlet-based distance measure, which is defined as the Euclidean
distance of the upper triangle values of the Graphlet Correlation
Matrices (GCM) of two networks (Yaveroglu et al., 2014).
The GCM of a network is a matrix with Spearman's correlations between the
network's node orbits (Hocevar and Demsar, 2016).
See calcGCD for details.
Value
Object of class microNetComp with the following
elements:
jaccDeg,jaccBetw,jaccClose,jaccEigen | Values of Jaccard's index for the centrality measures |
jaccHub | Jaccard index for the sets of hub nodes |
randInd | Adjusted Rand index |
randIndLCC | Adjusted Rand index for the largest connected component (LCC) |
gcd | Graphlet Correlation Distance (object of class gcd
returned by calcGCD) |
gcdLCC | Graphlet Correlation Distance for the LCC |
properties | List with calculated network properties |
propertiesLCC | List with calculated network properties of the LCC |
diffGlobal | Vectors with differences of global properties |
diffGlobalLCC | Vectors with differences of global properties for the LCC |
diffCent | Vectors with differences of the centrality values |
countMatrices | The two count matrices returned
by netConstruct |
assoMatrices | The two association matrices returned
by netConstruct |
dissMatrices | The two dissimilarity matrices returned
by netConstruct |
adjaMatrices | The two adjacency matrices returned
by netConstruct |
groups | Group names returned by netConstruct |
paramsProperties | Parameters used for network analysis |
Additional output if permutation tests are conducted:
pvalDiffGlobal | P-values of the tests for differential global properties |
pvalDiffGlobalLCC | P-values of the tests for differential global properties in the LCC |
pvalDiffCentr | P-values of the tests for differential centrality values |
pvalDiffCentrAdjust | Adjusted p-values of the tests for differential centrality values |
permDiffGlobal | nPerm x 10 matrix containing the absolute
differences of the ten global network properties (computed for the whole
network) for all nPerm permutations |
permDiffGlobalLCC | nPerm x 11 matrix containing the
absolute differences of the eleven global network properties (computed for
the LCC) for all nPerm permutations |
permDiffCentr | List with absolute differences of the four
centrality measures for all nPerm permutations. Each list contains
a nPerm x nNodes matrix.
|
References
\insertRefbenjamini2000adaptiveNetCoMi
\insertReffarcomeni2007someNetCoMi
\insertRefgill2010statisticalNetCoMi
\insertRefhocevar2016computationNetCoMi
\insertRefqannari2014significanceNetCoMi
\insertRefreal1996probabilisticNetCoMi
\insertRefyaveroglu2014revealingNetCoMi
See Also
summary.microNetComp, netConstruct,
netAnalyze
Examples
# Load data sets from American Gut Project (from SpiecEasi package)
data("amgut2.filt.phy")
# Split data into two groups: with and without seasonal allergies
amgut_season_yes <- phyloseq::subset_samples(amgut2.filt.phy,
SEASONAL_ALLERGIES == "yes")
amgut_season_no <- phyloseq::subset_samples(amgut2.filt.phy,
SEASONAL_ALLERGIES == "no")
amgut_season_yes
amgut_season_no
# Filter the 121 samples (sample size of the smaller group) with highest
# frequency to make the sample sizes equal and thus ensure comparability.
n_yes <- phyloseq::nsamples(amgut_season_yes)
# Network construction
amgut_net <- netConstruct(data = amgut_season_yes,
data2 = amgut_season_no,
measure = "pearson",
filtSamp = "highestFreq",
filtSampPar = list(highestFreq = n_yes),
filtTax = "highestVar",
filtTaxPar = list(highestVar = 30),
zeroMethod = "pseudoZO", normMethod = "clr")
# Network analysis
# Note: Please zoom into the GCM plot or open a new window using:
# x11(width = 10, height = 10)
amgut_props <- netAnalyze(amgut_net, clustMethod = "cluster_fast_greedy")
# Network plot
plot(amgut_props,
sameLayout = TRUE,
title1 = "Seasonal allergies",
title2 = "No seasonal allergies")
#--------------------------
# Network comparison
# Without permutation tests
amgut_comp1 <- netCompare(amgut_props, permTest = FALSE)
summary(amgut_comp1)
# With permutation tests (with only 100 permutations to decrease runtime)
amgut_comp2 <- netCompare(amgut_props,
permTest = TRUE,
nPerm = 100L,
cores = 1L,
storeCountsPerm = TRUE,
fileStoreCountsPerm = c("countsPerm1",
"countsPerm2"),
storeAssoPerm = TRUE,
fileStoreAssoPerm = "assoPerm",
seed = 123456)
# Rerun with a different adjustment method ...
# ... using the stored permutation count matrices
amgut_comp3 <- netCompare(amgut_props, adjust = "BH",
permTest = TRUE, nPerm = 100L,
fileLoadCountsPerm = c("countsPerm1",
"countsPerm2"),
seed = 123456)
# ... using the stored permutation association matrices
amgut_comp4 <- netCompare(amgut_props, adjust = "BH",
permTest = TRUE, nPerm = 100L,
fileLoadAssoPerm = "assoPerm",
seed = 123456)
# amgut_comp3 and amgut_comp4 should be equal
all.equal(amgut_comp3$adjaMatrices, amgut_comp4$adjaMatrices)
all.equal(amgut_comp3$properties, amgut_comp4$properties)
summary(amgut_comp2)
summary(amgut_comp3)
summary(amgut_comp4)
#--------------------------
# Use 'createAssoPerm' to create "permuted" count and association matrices
createAssoPerm(amgut_props, nPerm = 100,
computeAsso = TRUE,
fileStoreAssoPerm = "assoPerm",
storeCountsPerm = TRUE,
fileStoreCountsPerm = c("countsPerm1", "countsPerm2"),
append = FALSE, seed = 123456)
amgut_comp5 <- netCompare(amgut_props, permTest = TRUE, nPerm = 100L,
fileLoadAssoPerm = "assoPerm")
all.equal(amgut_comp3$properties, amgut_comp5$properties)
summary(amgut_comp5)
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