Runs correlation analysis pipeline

Runs correlation analysis pipeline

correlation_analysis(
  dataset_name = "placeholder",
  allstudies = "placeholder",
  celltypes = "placeholder",
  pvals = c(0.05, 0.025, 0.01, 0.001, 1e-04),
  data_names = "placeholder",
  alphaval = "placeholder",
  numPerms = "placeholder",
  numSubsets = "placeholder",
  output_path = getwd()
)

Arguments

dataset_name

name of the dataset used to select significant DEGs from (specified as a string, name as in allstudies)

allstudies

a list containing all the datasets (as SCE objects)

celltypes

a list containing the celltypes to compute mean correlation across

pvals

list of p-value cut-offs which will be used to select DEGs

data_names

names of the datasets as they appear in the correlation plot

alphaval

(alpha) transparency of the non-mean boxplots

numPerms

number of random permutations of the dataset used to select significant DEGs from

numSubsets

number of pairs of random subsets of the dataset used to select significant DEGs from

output_path

base path in which outputs will be stored Saves all plots and DGE analysis outputs in the appropriate directories