🤔 Aba | 全自动biomarker分析神包！~（原作者用这

作者: 生信漫卷 | 来源:发表于2022-12-13 14:00 被阅读0次

写在前面

今天介绍一个Github上的神包吧, 主要是用于Biomarker的临床分析, 原作者用这个包已经发了3篇Nature了, 一起看看吧:👇

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在一些针对Biomarker的临床研究中, 我们常常需对Biomarker进行模型拟合, 预测效果评估等等.🥰
这个包可以完美解决这些问题, 并且直接输出发表级图表, 简单介绍一下用法给大家吧.🥳

用到的包

rm(list = ls())
#devtools::install_github("ncullen93/abaR")
library(aba)
library(tidyverse)
library(ggsci)

示例数据

dat <- adnimerge %>% 
  dplyr::filter(VISCODE == 'bl')

DT::datatable(dat)

变量一览

看一下都有什么变量, 都是什么类型. 🤞

str(dat)

建立模型

5.1 原函数

大家可以通过这种方式来建立模型.

  aba_model(
   data = NULL,
   groups = NULL,
   outcomes = NULL,
   predictors = NULL,
   covariates = NULL,
   stats = NULL,
   evals = NULL,
   include_basic = TRUE
 )

5.2 pipeline形式

这里也提供了pipeline的形式来编写代码, 个人也是更倾向于这种方式, 大家试一下吧. 😏

我们在这里设定两个结局指标: ConvertedToAlzheimers和CSF_ABETA_STATUS_bl.🤒
两个预测指标, 即Biomarker, PLASMA_PTAU181_bl和PLASMA_NFL_bl. 🤫

模型为logistic regression. 📈

model <- aba_model() %>% 
  set_data(dat) %>% 
  set_groups(DX_bl %in% c('MCI','AD')) %>% 
  set_outcomes(ConvertedToAlzheimers, CSF_ABETA_STATUS_bl) %>% 
  set_predictors(
    PLASMA_PTAU181_bl,
    PLASMA_NFL_bl,
    c(PLASMA_PTAU181_bl, PLASMA_NFL_bl)
  ) %>% 
  set_covariates(AGE, GENDER, EDUCATION) %>% 
  set_stats(stat_glm(std.beta=T))

model

Note! 这里我们注意下如何进行Biomarker的联合应用, 可写为 c(PLASMA_PTAU181_bl, PLASMA_NFL_bl). 😘

5.3 拟合

model <- model %>% 
  fit()
model

5.4 模型数据

拟合完以后我们就获得了模型的结果, 大家可以大致看一下.🤓

model_summary <- model %>% 
  summary()

model_summary

模型结果的可视化

这个包提供了很多可视化的参数, 可以直接将summary的结果传递给画图函数, 非常简单. 😘

6.1 coeffficients可视化

这里需要说明一下, 函数内自带的配色只有4种, 即jama, nature, lancet, none.
但是大家可以按照ggplot语法更改颜色.🤜

model_summary %>% 
  aba_plot_coef(coord_flip=T,
                palette = 'nature')

6.2 AUC可视化

看看各个模型的AUC吧.😗

model_summary %>% 
  aba_plot_metric(palette = 'nature')

6.3 ROC可视化

model_summary %>% 
  aba_plot_roc()

6.4 Risk density plot

批量出图, 大家想看哪个predictor的Risk density plot就提取哪个吧. 🤪

fig <- model %>%
  aba_plot_risk_density()
fig

随便提取一个看看吧~~~😉

fig$fig[1]

补充一下

这个包还有很多其他强大的功能，大家可以去进一步地探索一下。😘

欢迎大家留言说一下其他强大的函数哦~

这里附上所有函数官方解释：👇

aba_adjust()

Create an aba_adjust object.

aba_control()

Create an aba control object.

aba_demographics()

Create a demographics table from a fitted aba model.

aba_diagnosticpower()

Caclulate diagnostic power based on a fitted aba model

aba_emmeans()

Calculated estimated marginal means.

aba_evaluate()

Evaluate a fitted aba model on new data

aba_fit()

Fit an aba model.

aba_longpower()

Run power analysis on a longitudinal-based aba model.

aba_model()

Create an aba model.

aba_plot()

Plot an aba object

aba_plot_coef()

Plot coefficients of an aba model summary

aba_plot_metric()

Plot metrics of an aba model summary

aba_plot_predictor_risk()

Plot predictor values versus predicted risk from fitted aba model

aba_plot_risk_density()

Plot risk density split by binary outcome class

aba_plot_roc()

Plot ROC curves from an aba model

aba_predict()

Get individual predictions from a fitted aba model

aba_read()

Read an aba object from file

aba_robust()

Evaluate the robustness of an aba model to systematic and random error.

aba_screen()

Create an aba screen object.

aba_selection()

Run model selection on an aba model.

aba_summary()

Summarise a fitted aba model.

aba_write()

Write an aba object to file.

adnimerge

A sample of ADNI data in long format

all_combos()

Create all possible combinations of a set of variables

all_levels()

Create groups from all levels of one or more variables

as_reactable()

Convert an aba summary to a interactive react table

as_reactable(*<abaSummary>*)

Convert an aba summary to a interactive react table

as_table()

Convert an aba summary to a nicely formatted table

as_table(*<abaSummary>*)

Convert an aba summary to a nicely formatted table

eval_boot()

Create a bootstrap evaluator

eval_cv()

Create a cross validation evaluator

eval_standard()

Create a standard evaluator

eval_traintest()

Create a train-test evaluator

everyone()

Use all data rows as a group in an aba model.

fit(*<abaModel>*)

Fit an aba model.

predict(*<abaModel>*)

Get individual predictions from a fitted aba model

set_covariates()

Set the covariates of an aba model.

set_data()

Set the data of an aba model

set_evals()

Set the evals of an aba model

set_groups()

Set the groups of an aba model.

set_outcomes()

Set the outcomes of an aba model.

set_predictors()

Set the predictors of an aba model.

set_stats()

Set the stats of an aba model

stat_ancova()

Create an ancova stat object.

stat_cox()

Create a glm stat object.

stat_glm()

Create a glm stat object.

stat_lm()

Create an lm stat object.

stat_lme()

Create an lme stat object.

stat_lmer()

Create an lmer stat object.

stat_mmrm()

Create an mmrm stat object.

stat_retest()

Create a retest stat object.

stat_roc()

Create a roc stat object.

theme_aba()

Custom aba ggplot2 theme

<center>最后祝大家早日不卷!~</center>

点个在看吧各位~ ✐.ɴɪᴄᴇ ᴅᴀʏ 〰

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