教學手冊：學習手冊

MaAsLin2

# BiocManager::install("Maaslin2",force = TRUE)library(Maaslin2)
# 用的是相對豐度，行名為-ID行樣本,列為細菌
input_data = system.file("extdata", "HMP2_taxonomy.tsv", package="Maaslin2") # The abundance table file
input_data
# 行名為-ID行樣本
input_metadata = system.file("extdata", "HMP2_metadata.tsv", package="Maaslin2") # The metadata table file
input_metadatadf_input_data = read.table(file             = input_data,header           = TRUE,sep              = "\t", row.names        = 1,stringsAsFactors = FALSE)
df_input_data[1:5, 1:5]df_input_metadata = read.table(file             = input_metadata, header           = TRUE, sep              = "\t", row.names        = 1,stringsAsFactors = FALSE)
df_input_metadata[1:5, ]fit_data = Maaslin2(input_data     = input_data, input_metadata = input_metadata, min_prevalence = 0,normalization  = "NONE",output         = "demo_output", fixed_effects  = c("diagnosis", "dysbiosis"),reference      = c("diagnosis,nonIBD")) # 列名-對照組