merged_ewce: Multiple EWCE results from multiple studies

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Multiple EWCE results from multiple studies

Description

merged_ewce combines enrichment results from multiple studies targetting the same scientific problem

Usage

merged_ewce(results, reps = 100)

Arguments

results	a list of EWCE results generated using add_res_to_merging_list.
reps	Number of random gene lists to generate (Default=100 but should be >=10,000 for publication-quality results).

Value

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.

Examples

# Load the single cell data
ctd <- ewceData::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 <- ewceData::tt_alzh_BA36()
tt_alzh_BA44 <- ewceData::tt_alzh_BA44()

# Run EWCE analysis
tt_results_36 <- EWCE::ewce_expression_data(
    sct_data = ctd,
    tt = tt_alzh_BA36,
    thresh = thresh,
    annotLevel = 1,
    reps = reps,
    ttSpecies = "human",
    sctSpecies = "mouse"
)
tt_results_44 <- EWCE::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 <- EWCE::add_res_to_merging_list(tt_results_36)
results <- EWCE::add_res_to_merging_list(tt_results_44, results)

# Perform the merged analysis
# For publication reps should be higher
merged_res <- EWCE::merged_ewce(
    results = results,
    reps = 2
)
print(merged_res)

NathanSkene/EWCE documentation built on April 10, 2024, 1:02 a.m.