merged_ewce {EWCE} | R Documentation |
merged_ewce
combines enrichment results from multiple studies
targetting the same scientific problem
merged_ewce(results, reps = 100)
results |
a list of EWCE results generated using
|
reps |
Number of random gene lists to generate (default=100 but should be over 10000 for publication quality results) |
dataframe in which each row gives the statistics (p-value, fold change and number of standard deviations from the mean) associated with the enrichment of the stated cell type in the gene list
library(ewceData) # Load the single cell data ctd <- ctd() # Use 3 bootstrap lists for speed, for publishable analysis use >10000 reps <- 3 # Use 5 up/down regulated genes (thresh) for speed, default is 250 thresh = 5 # Load the data tt_alzh_BA36 <- tt_alzh_BA36() tt_alzh_BA44 <- tt_alzh_BA44() # Run EWCE analysis tt_results_36 <- ewce_expression_data( sct_data = ctd, tt = tt_alzh_BA36, thresh= thresh, annotLevel = 1, reps=reps, ttSpecies = "human", sctSpecies = "mouse" ) tt_results_44 <- ewce_expression_data( sct_data = ctd, tt = tt_alzh_BA44, thresh = thresh, annotLevel = 1, reps=reps, ttSpecies = "human", sctSpecies = "mouse" ) # Fill a list with the results results <- add_res_to_merging_list(tt_results_36) results <- add_res_to_merging_list(tt_results_44, results) # Perform the merged analysis # For publication reps should be higher merged_res <- merged_ewce(results, reps = 2) print(merged_res)