calc_fisher | R Documentation |
Use one-tailed Fisher's exact test to calcualte overlap enrichment between proteomic data and other datasets (e.g. InWeb, gene lists, etc.)
calc_fisher(df, listDf, intersectDf, bait = NULL)
df |
data.frame containing proteomic data, with gene and significant columns |
listDf |
data.frame containing data to overlap, with listName, gene and significant columns |
intersectDf |
data.frame contaning listName and intersectN columnsl intersectN = vector of boolean variables indicating if total population should be intersect of the two datasets |
bait |
name of bait protein |
list of data.frame and list. Data.frame contains list_name, overlap_count, dfOnly_count, listOnly_count, neither_count, population_count, pvalue. List of lists (for each listName) contains genes names corresponding to each group (overlap_genes, dfOnly_genes, listOnly_genes, neither_genes, population_genes).
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