“CausCor” is an R package for correlation analysis to estimate causality. Particularly, it is useful for detecting the metabolites that would be altered by the gut bacteria.
CausCor can be installed from CRAN,
or from GitHub,
This package has following functions. - 2 type filtering functions to get correlation lists: filter_n(), filter_40() - All correlation coefficients and R2 scores are calculated by Overlap samples only. Overlap is a pair that both bacteria and metabolite abundance are non-zero. - filter_n() is the filtering function with thresholds for Spearman correlation coefficient, Overlap, and R2 score. - filter_40() is the more specialized function for causal estimation. Overlap is fixed between 40% and 60% of the total samples by default. (If necessary, you can change them.) And only extract the pattern that the samples who have the bacteria always have the metabolite in a certain pair.
save_text()plot_16()Prepare two category tables and read them as dataframe. The first column has the names of features, and second and subsequent columns have the values for each sample. The order of the samples must be aligned in the two datasets.
All filtering functions need microbiome table, metabolome table and two category names (“genus” and “metabolome”, etc.).
filter_n() requires the setting of thresholds for Spearman correlation coefficient, Overlap, and R2 score.
# Example
list_n <- filter_n(microbiome_table, metabolome_table, "genus", "metabolome",
0.6, # Spearman
5, # Overlap
0.3) # R2 Scorefilter_40() requires the setting of thresholds for Spearman correlation coefficient and R2 score. If necessary, you can set minimum or maximum Overlap.# Example
list_40 <- filter_40(microbiome_table, metabolome_table, "genus", "metabolome",
0.6, # Spearman
0.3) # R2 Score
list_5to10 <- filter_40(microbiome_table, metabolome_table, "genus", "metabolome",
0.6, # Spearman
0.3, # R2 Score
min_sample = 5, # minimum Overlap
max_sample = 10) # maximum Overlapsave_text().# Example
# You can choose file type from "excel", "csv", "tsv"
save_text(list_n, "list_n.xlsx", "excel")plot_16().