Description Usage Arguments Details Value References See Also Examples
View source: R/associateData-method.R
Function to estimate differences in expression initation of trajectories to identify associations between time course 'omics' data.
1 | associateData(data1,data2,numCores)
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data1 |
|
data2 |
optional an additional |
numCores |
alternative |
associateData() takes as input two data sets of interest and performs a pairwise associations comparison between features using a fast Fourier transform approach to detect delays (also called 'associations') between the different features. Note that the argument ‘numCores' indicates the number of CPUs and is detected by default in the function to perform parallelization. The final result is a table with a row for each pairwise comparison. The output presents the dynOmics estimated delay between two features, the p-value ('p') and correlation coefficient ('cor') from a Pearson’s test, before and after the time profiles have been realigned according to the dynOmics estimated delay.
associateData returns an object of class associations
containing the following components:
Feature1 character
the colnames or the index of data1.
Feature2 character
the colnames or the index of data2.
delay numeric
estimated delay between feature1 and feature2.
pBefore numeric
p-value of the test for association before applying the predicted time shift.
pAfter numeric
p-value of the test for association after applying the predicted time shift.
corBefore numeric
Pearson correlation before applying the predicted time shift.
corAfter numeric
Pearson correlation after applying the predicted time shift.
Straube J., Bernard A., Huang B.E., Le Cao K.-A.(2017). DynOmics to identify delays and co-expression patterns across time course experiments Scientific Reports
summary.associations
, plot.associations
1 2 3 4 5 6 7 8 | ## Not run:
data(Metabolites)
data(Transcripts)
associations <- associateData(Metabolites[,1],Transcripts[,c(1:50)])
#summary(associations)
#plot(associations,Metabolites,Transcripts,feature1=1)
## End(Not run)
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