Phyloseq。如何测试丰度差异 [英] Phyloseq. How to test abundance difference

问题描述

图书馆phyoloseq数据= Globalpatterns

Library phyoloseq Data= Globalpatterns

GP = filter_taxa(GlobalPatterns, function(x) sum(x > 3) > (0.2*length(x)), TRUE)

定义人类与非人类分类变量，并将此新变量添加到样本数据：

Define a human versus non-human categorical variable, and add this new variable to sample data:

sample_data(GP)$human = factor( get_variable(GP, "SampleType") %in% c("Feces", "Mock", "Skin", "Tongue") )

将丰度标准化为中位数测序深度

Standardize abundances to the median sequencing depth

total = median(sample_sums(GP))
standf = function(x, t=total) round(t * (x / sum(x)))
gps = transform_sample_counts(GP, standf)

使用3.0的截止值对变异系数过滤分类群

Filter the taxa using a cutoff of 3.0 for the Coefficient of Variation

gpsf = filter_taxa(gps, function(x) sd(x)/mean(x) > 3.0, TRUE)

    Subset the data to Bacteroidetes, used in some plots
    gpsfb = subset_taxa(gpsf, Phylum=="Bacteroidetes")

绘制数据

Plotting the the data

title = "plot_bar; Bacteroidetes-only"
plot_bar(gpsfb, "SampleType", "Abundance", title=title)

问题：什么我需要编写代码来测试特定样本类型的拟杆菌的丰度差异，如当前的例子中使用的是ANOVA？



我尝试过：



目前gpsfb是phylseq对象，所以现在我迷路了

Question: What code do i need to write, to test difference in abundance of Bacteroidetes for specific sampletype like feces with ect ANOVA with current example?

What I have tried:

Currently gpsfb is phylseq object, so now i am lost

推荐答案

human = factor（get_variable（GP，SampleType）％in％c（粪便，模拟，皮肤，舌头））

human = factor( get_variable(GP, "SampleType") %in% c("Feces", "Mock", "Skin", "Tongue") )

标准化丰度到中位数测序深度

Standardize abundances to the median sequencing depth

total = median(sample_sums(GP))
standf = function(x, t=total) round(t * (x / sum(x)))
gps = transform_sample_counts(GP, standf)

过滤分类群使用3.0的截断值作为变异系数

Filter the taxa using a cutoff of 3.0 for the Coefficient of Variation

gpsf = filter_taxa(gps, function(x) sd(x)/mean(x) > 3.0, TRUE)

    Subset the data to Bacteroidetes, used in some plots
    gpsfb = subset_taxa(gpsf, Phylum=="Bacteroidetes")

绘制数据

Plotting the the data

title = "plot_bar; Bacteroidetes-only"
plot_bar(gpsfb, "SampleType", "Abundance", title=title)

问题：什么我需要编写代码来测试特定样本类型的拟杆菌的丰度差异，如当前的例子中使用的是ANOVA？



我尝试过：



目前gpsfb是phylseq对象，所以现在我迷路了

Question: What code do i need to write, to test difference in abundance of Bacteroidetes for specific sampletype like feces with ect ANOVA with current example?

What I have tried:

Currently gpsfb is phylseq object, so now i am lost

这篇关于Phyloseq。如何测试丰度差异的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！