The function tests whether graphlet correlations (entries of
the GCM) are significantly different from zero.
If two GCMs are given, the graphlet correlations of the two networks are
tested for being significantly different, i.e., Fishers z-test
is performed to test if the absolute differences between graphlet
correlations are significantly different from zero.
Usage
testGCM(
obj1,
obj2 = NULL,
adjust = "adaptBH",
lfdrThresh = 0.2,
trueNullMethod = "convest",
alpha = 0.05,
verbose = TRUE
)
Arguments
- obj1
object of class
GCM
orGCD
returned bycalcGCM
orcalcGCD
. See details.- obj2
optional object of class
GCM
returned bycalcGCM
. See details.- adjust
character indicating the method used for multiple testing adjustment. 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 byp.adjust
.- lfdrThresh
defines a threshold for the local fdr if "lfdr" is chosen as method for multiple testing correction. Defaults to 0.2 meaning that differences with a corresponding local fdr less than or equal to 0.2 are identified as significant.
- 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 themethod
argument ofpropTrueNull
: "convest" (default), "lfdr", "mean", and "hist". Can alternatively be "farco" for the "iterative plug-in method" proposed by Farcomeni (2007).- alpha
numeric value between 0 and 1 giving the desired significance level.
- verbose
logical. If
TRUE
(default), progress messages are printed.
Value
A list with the following elements:
gcm1 | Graphlet Correlatoin Matrix GCM1 |
pvals1 | Matrix with p-values (H0: gc1_ij = 0) |
padjust1 | Matrix with adjusted p-values |
Additional elements if two GCMs are given:
gcm2 | Graphlet Correlatoin Matrix GCM2 |
pvals2 | Matrix with p-values (H0: gc2_ij = 0) |
padjust2 | Matrix with adjusted p-values |
diff | Matrix with differences between graphlet correlations (GCM1 - GCM2) |
absDiff | Matrix with absolute differences between graphlet correlations (|GCM1 - GCM2|) |
pvalsDiff | Matrix with p-values (H0: |gc1_ij - gc2_ij| = 0) |
pAdjustDiff | Matrix with adjusted p-values |
sigDiff | Same as diff , but non-significant differences
are set to zero. |
sigAbsDiff | Same as absDiff , but non-significant
values are set to zero. |
Details
By applying Student's t-test to the Fisher-transformed correlations,
all entries of the GCM(s) are tested for being
significantly different from zero:
H0: gc_ij = 0 vs. H1: gc_ij != 0,
with gc_ij being the graphlet correlations.
If both GCMs are given or obj1
is of class GCD
, the absolute
differences between graphlet correlations are tested for being different
from zero using Fisher's z-test. The hypotheses are:
H0: |d_ij| = 0 vs. H1: |d_ij| > 0,
where d_ij = gc1_ij - gc2_ij