如何在R-微生物群上对流行人群进行性别细分

Question

我是R的新手，我正在使用一个脚本，它基于国家将atlas1006微生物组数据分成3组疾病流行率(低，中，高)。我想将每一组细分为:低，中，高，每组分为男性和女性，即低男性，低女性，中等男性，中等女性，高男性，高女性。我想保持3个现有的小组低，中，高也。这是将数据分为低、中、高的代码：

# Create mnd variable
# grabs the nationality from phyloseq
test <- get_variable(pseq, "nationality" )

# check you've installed this library
library(forcats)

# this collapses the two variables into a new variable AB in this case. The command for multiple changes is fct_collapse(x, AB = c("A","B"), DE = c("D","E"))
# test <- fct_collapse(test, LOW = c("Scandinavia","EasternEurope") , MEDIUM = c("SouthEurope","CentralEurope", "UKIE"), HIGH = c("US") )

test <- fct_collapse(test, LOW = c("EasternEurope","Scandinavia") , MEDIUM = c("SouthEurope","CentralEurope", "UKIE" ), HIGH = c("US"))

# reorder
test <- factor(test, levels = (c("LOW", "MEDIUM", "HIGH")))
levels(test)

# creates a new variable in the phyloseq called mnd
sample_data(pseq)$mnd = test

# checks that it has worked.
get_variable(pseq, "mnd")

对于如何在这里进行性别划分，有什么建议吗？

Answer 1

如果您想创建单独的phyloseq对象，例如包含high组和females.you，可以使用subset_samples

subset_samples(pseq, mnd=="high" & gender_variable == "female")