.permTestDiffAsso | R Documentation |
The function implements procedures to test whether pairs of taxa are differentially associated, whether a taxon is differentially associated to all other taxa, or whether two networks are differentially associated between two groups as proposed by Gill et al.(2010).
.permTestDiffAsso(
countMat1,
countMat2,
countsJoint,
normCounts1,
normCounts2,
assoMat1,
assoMat2,
paramsNetConstruct,
method = c("connect.pairs", "connect.variables", "connect.network"),
fisherTrans = TRUE,
pvalsMethod = "pseudo",
adjust = "lfdr",
adjust2 = "holm",
trueNullMethod = "convest",
alpha = 0.05,
lfdrThresh = 0.2,
nPerm = 1000,
matchDesign = NULL,
callNetConstr = NULL,
cores = 4,
verbose = TRUE,
logFile = "log.txt",
seed = NULL,
fileLoadAssoPerm = NULL,
fileLoadCountsPerm = NULL,
storeAssoPerm = FALSE,
fileStoreAssoPerm = "assoPerm",
storeCountsPerm = FALSE,
fileStoreCountsPerm = c("countsPerm1", "countsPerm2"),
assoPerm = NULL
)
countMat1, countMat2 |
matrices containing microbiome data (read counts) of group 1 and group 2 (rows represent samples and columns taxonomic units, respectively). |
countsJoint |
joint count matrices before preprocessing |
normCounts1, normCounts2 |
normalized count matrices. |
assoMat1, assoMat2 |
association matrices corresponding to the two count
matrices. The associations must have been estimated from the count matrices
|
paramsNetConstruct |
parameters used for network construction. |
method |
character vector indicating the tests to be performed. Possible
values are |
fisherTrans |
logical indicating whether the correlation values should be Fisher-transformed. |
pvalsMethod |
currently only |
adjust |
multiple testing adjustment for the tests for differentially
correlated pairs of taxa; possible values are "lfdr" (default) for local
false discovery rate correction (via |
adjust2 |
multiple testing adjustment for the tests if a taxa pair is
differentially correlated to all other taxa; possible methods are those
provided by |
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 |
alpha |
significance level |
lfdrThresh |
defines a threshold for the local fdr if "lfdr" is chosen as method for multiple testing correction; defaults to 0.2, which means that correlations with a corresponding local fdr less than or equal to 0.2 are identified as significant |
nPerm |
number of permutations |
matchDesign |
Numeric vector with two elements specifying an optional
matched-group (i.e. matched-pair) design, which is used for the permutation
tests in |
callNetConstr |
call inherited from |
cores |
number of CPU cores (permutation tests are executed parallel) |
verbose |
if |
logFile |
character string naming the log file within which the current iteration number is stored |
seed |
an optional seed for reproducibility of the results |
fileLoadAssoPerm |
character giving the name (without extenstion)
or path of the file storing the "permuted" association/dissimilarity
matrices that have been exported by setting |
fileLoadCountsPerm |
character giving the name (without extenstion)
or path of the file storing the "permuted" count matrices that have been
exported by setting |
storeAssoPerm |
logical indicating whether the association (or
dissimilarity) matrices for the permuted data should be stored in a file.
The filename is given via |
fileStoreAssoPerm |
character giving the file name to store a matrix containing a matrix with associations/dissimilarities for the permuted data. Can also be a path. |
storeCountsPerm |
logical indicating whether the permuted count matrices
should be stored in 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. |
assoPerm |
not used anymore. |
gill2010statisticalNetCoMi
\insertRefknijnenburg2009fewerNetCoMi
diffnet
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