The information is currently stored in
GRN@connections$TF_genes.filtered. Note that raw p-values are not adjusted.
add_TF_gene_correlation( GRN, corMethod = "pearson", addRobustRegression = FALSE, nCores = 1, forceRerun = FALSE )
Object of class
pearson. Method for calculating the correlation coefficient. See cor for details.
FALSE. EXPERIMENTAL. Default
Use a robust regression in addition to a non-robust one? Significantly increases overall running time.
If set to
TRUE, the package
robust is required (as it is listed under
Suggests, it may not be installed).
Integer >0. Default 1. Number of cores to use.
A value >1 requires the
BiocParallel package (as it is listed under
Suggests, it may not be installed yet).
FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.
GRN object, with additional information added from this function.
# See the Workflow vignette on the GRaNIE website for examples GRN = loadExampleObject() #> Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds #> Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing! GRN = add_TF_gene_correlation(GRN, forceRerun = FALSE) #> INFO [2023-03-06 16:39:14] Data already exists in object. Set forceRerun = TRUE to regenerate and overwrite. #> INFO [2023-03-06 16:39:14] Finished successfully. Execution time: 0 secs