runDESeq2: Runs differential analysis using DESeq2 for a Location...

In blue-moon22/resistomeAnalysis: Resistome Analysis

Description

Runs differential analysis using DESeq2 for a Location between paired sample types

Usage

runDESeq2(df, Location, compare_samples = c("stool", "dorsum of tongue"))

Arguments

Location	A string of a Location that is found in the Location column of df_map
compare_samples	A character vector of length two of sample types to compare
df_map	A dataframe of combined non-subsampled or subsampled mapping data and metadata

Value

A list of length two of a dataframe of DESeq2 results and a character vector of sample types compared in DESeq2

Examples

df_map <- readMappingData("/home/vicky/Documents/CHMI/Resistome-paper/resistomeAnalysis/db/MAPPING_DATA/nonsubsampled_merged.csv", without_US_duplicates = TRUE)

output_list <- runDESeq2(df_map, "US", c("stool", "dorsum of tongue"))

blue-moon22/resistomeAnalysis documentation built on Jan. 17, 2020, 4:15 a.m.