getSpearmanCorrelation: Get a dataframe of correlated ARGs and taxa using Spearman's...
In blue-moon22/resistomeAnalysis: Resistome Analysis

Description Usage Arguments Value Examples

Get a dataframe of correlated ARGs and taxa using Spearman's Correlation

1	getSpearmanCorrelation(data, ids = NA, taxon_level, taxon_ignore)

`data`	A dataframe of combined non-subsampled mapping data and metadata
`ids`	A character vector of sample IDs
`taxon_level`	A string representing the taxon level to apply Spearman's Correlation, where k is Kingdom, p is Phylum, c is Class, o is Order, f is Family, g is Genus, s is Species and t is Strain
`taxon_ignore`	A string representing the taxon level to not include in Spearman's Correlation, where k is Kingdom, p is Phylum, c is Class, o is Order, f is Family, g is Genus, s is Species, t is Strain and "" is don't ignore any taxa. It has to be a taxon after taxon_level.

A dataframe containing correlated ARGs and taxa, rho and adjusted p-values

df_map <- readMappingData("/home/vicky/Documents/CHMI/Resistome-paper/resistomeAnalysis/db/MAPPING_DATA/nonsubsampled_merged.csv", without_US_duplicates = TRUE)
metaphlan <- read.csv("/home/vicky/Documents/CHMI/Resistome-paper/resistomeAnalysis/db/METAPHLAN/metaphlan.csv", stringsAsFactors = FALSE, row.names = 1)
metaphlan_rpkm <- combineMetaphlanandARG(df_map, metaphlan)

high_cor_uk_oral <- getSpearmanCorrelation(metaphlan_rpkm, ids = unique(df_map$ID[df_map$Cohort == "Twin" & df_map$sample_type == "saliva"]), taxon_level = "t", taxon_ignore = "@@")