oracle rodm包,R语言---使用RTCGA包获取TCGA数据---笔记整理

原文链接：https://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&mid=2247486585&idx=1&sn=3035f6420904aad2c8161b362cdeb472&chksm=9b484cc2ac3fc5d479fc5bce3d68d4666b763652a21a55b281aad8c0c4df9b56b4d3b353cc4c&scene=21#wechat_redirect

1.RTCGA相关包的下载及使用？

(1)相关包的下载：(原文中的代码在我的电脑上执行的有些问题，故包的下载代码修改如下：)

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("RTCGA")

BiocManager::install("RTCGA.clinical")

BiocManager::install("RTCGA.rnaseq")

BiocManager::install("RTCGA.mRNA")

BiocManager::install("RTCGA.mutations")

(2)包的使用代码为：library(包的名称)

2.RTCGA包的工作流程？(图片是从原文中截取的)

3.指定任意基因从任意癌症里面获取芯片表达数据

library(RTCGA)

library(RTCGA.mRNA)

#收集TCGA数据集的表达式(表达量数据)(Gather Expressions for TCGA Datasets)

expr

extract.cols = c("GATA3", "PTEN", "XBP1","ESR1", "MUC1"))

#print(expr)

#统计表达式出现的次数

nb_samples

print(nb_samples)

结果如下：

观察可得，上述结果标识太过复杂，为了更方便地展示结果，添加代码如下：

#简化一下标识，方便可视化展现

#gsub函数为字符串替换函数

expr$dataset

#paste0函数为字符串连接函数

expr$bcr_patient_barcode

print(expr)

结果如下：

4.绘制指定基因在不同癌症的表达量区别boxplot

library(ggplot2)

library(ggpubr)# load the packages need load ggplot2 packages first

# GATA3,为expr的一列值

ggboxplot(expr, x = "dataset", y = "GATA3",

title = "GATA3", ylab = "Expression",

color = "dataset", palette = "jco")

# PTEN,为expr的一列值

ggboxplot(expr, x = "dataset", y = "PTEN",

title = "PTEN", ylab = "Expression",

color = "dataset", palette = "jco")

图形如下：

加入P值(显著性差异)信息：

为了便于观察信息，可以加入其它的boxplot参数。

label.select.criteria 3.9 & `x` %in% c('BRCA', 'OV')")

ggboxplot(expr, x = "dataset",

y = c("GATA3", "PTEN", "XBP1"),

combine = TRUE,

color = "dataset", palette = "jco",

ylab = "Expression",

label = "bcr_patient_barcode", # column containing point labels

label.select = label.select.criteria, # Select some labels to display

font.label = list(size = 9, face = "italic"), # label font

repel = TRUE # Avoid label text overplotting

)

效果如下：

有的情况下为了便于观察，可以进行翻转：

ggboxplot(expr, x = "dataset", y = "GATA3",

title = "GATA3", ylab = "Expression",

color = "dataset", palette = "jco",

rotate = TRUE)

效果图如下：

5.指定任意基因从任意癌症里面获取测序表达数据

library(RTCGA)

library(RTCGA.rnaseq)

expr

extract.cols = c("GATA3|2625", "PTEN|5728", "XBP1|7494","ESR1|2099", "MUC1|4582"))

print(expr)

#

nb_samples

#绘图

library(ggpubr)

ggboxplot(expr, x = "dataset", y = "PTEN|5728",

title = "ESR1|2099", ylab = "Expression",

color = "dataset", palette = "jco")

效果图：

6.用全部的rnaseq的表达数据来做主成分分析

library(RTCGA)

library(RTCGA.rnaseq)#加载此包需先加载RTCGA包

library(dplyr)

expressionsTCGA(BRCA.rnaseq, OV.rnaseq, HNSC.rnaseq) %>%

dplyr::rename(cohort = dataset) %>%

filter(substr(bcr_patient_barcode, 14, 15) == "01") -> BRCA.OV.HNSC.rnaseq.cancer

#主成分分析函数

pcaTCGA(BRCA.OV.HNSC.rnaseq.cancer, "cohort") -> pca_plot

plot(pca_plot)

效果图：

7.用5个基因在3个癌症的表达量做主成分分析

expr %>%

filter(substr(bcr_patient_barcode, 14, 15) == "01") -> rnaseq.5genes.3cancers

DT::datatable(rnaseq.5genes.3cancers)

#主成分分析

#pcaTCGA(rnaseq.5genes.3cancers, "dataset") -> pca_plot

#plot(pca_plot)

8.用突变数据做生存分析

library(RTCGA.mutations)

library(dplyr)

library(survminer)

mutationsTCGA(BRCA.mutations, OV.mutations) %>%

filter(Hugo_Symbol == 'TP53') %>%

filter(substr(bcr_patient_barcode, 14, 15) ==

"01") %>% # cancer tissue

mutate(bcr_patient_barcode =

substr(bcr_patient_barcode, 1, 12)) ->

BRCA_OV.mutations

library(RTCGA.clinical)

survivalTCGA(

BRCA.clinical,

OV.clinical,

extract.cols = "admin.disease_code"

) %>%

dplyr::rename(disease = admin.disease_code) ->

BRCA_OV.clinical

BRCA_OV.clinical %>%

left_join(

BRCA_OV.mutations,

by = "bcr_patient_barcode"

) %>%

mutate(TP53 =

ifelse(!is.na(Variant_Classification), "Mut","WILDorNOINFO")) ->

BRCA_OV.clinical_mutations

BRCA_OV.clinical_mutations %>%

select(times, patient.vital_status, disease, TP53) -> BRCA_OV.2plot

kmTCGA(

BRCA_OV.2plot,

explanatory.names = c("TP53", "disease"),

break.time.by = 400,

xlim = c(0,2000),

pval = TRUE) -> km_plot

print(km_plot)

效果图如下：

9.多个基因在多种癌症的表达量热图

library(RTCGA.rnaseq)

# perfrom plot

# library(dplyr) if did not load at start

expressionsTCGA(

ACC.rnaseq,

BLCA.rnaseq,

BRCA.rnaseq,

OV.rnaseq,

extract.cols =

c("MET|4233",

"ZNF500|26048",

"ZNF501|115560")

) %>%

dplyr::rename(cohort = dataset,

MET = `MET|4233`) %>%

#cancer samples

filter(substr(bcr_patient_barcode, 14, 15) ==

"01") %>%

mutate(MET = cut(MET,

round(quantile(MET, probs = seq(0,1,0.25)), -2),

include.lowest = TRUE,

dig.lab = 5)) -> ACC_BLCA_BRCA_OV.rnaseq

ACC_BLCA_BRCA_OV.rnaseq %>%

select(-bcr_patient_barcode) %>%

group_by(cohort, MET) %>%

summarise_each(funs(median)) %>%

mutate(ZNF500 = round(`ZNF500|26048`),

ZNF501 = round(`ZNF501|115560`)) ->

ACC_BLCA_BRCA_OV.rnaseq.medians

heatmapTCGA(ACC_BLCA_BRCA_OV.rnaseq.medians,

"cohort", "MET", "ZNF500",

title = "Heatmap of ZNF500 expression")

效果图：

10.知识点总结

(1)R语言中的table函数：主要有两个作用：

1°统计每个数据出现的次数。aq：

2°实现混淆矩阵。(ps：暂未理解)

(2)R语言中的gsub函数：R语言中的sub()函数和gsub()函数均为字符串替换函数，两者的区别在于sub()函数只会替换最初匹配到的字符串，且只匹配一次，而gsub()函数会替换掉所有匹配的字符串。gsub()函数的具体用法为gsub(“替换的目标字符串”，"被替换的字符串"，父串)。

(3)R语言中的paste0函数：paste()函数和paste0()函数均为字符串连接函数。区别在于连接的两个字符串之间的符号是否为空。

(4)R语言的ggpubr包中的重要函数。

1°ggboxplot函数：该函数绘制的是箱型图。参数如下：

ggboxplot(data, x, y, combine = FALSE, merge = FALSE, color = "black",

fill = "white", palette = NULL, title = NULL, xlab = NULL,

ylab = NULL, facet.by = NULL, panel.labs = NULL,

short.panel.labs = TRUE, linetype = "solid", size = NULL, width = 0.7,

notch = FALSE, select = NULL, remove = NULL, order = NULL,

add = "none", add.params = list(), error.plot = "pointrange",

label = NULL, font.label = list(size = 11, color = "black"),

label.select = NULL, repel = FALSE, label.rectangle = FALSE,

ggtheme = theme_pubr(), ...)

2°ggpubr中的两个关键函数：compare_means():做统计分析；stat_compare_means()：自行完成统计分析，并在图中加入显著性信息。

(5)R语言中的dplyr包：https://blog.csdn.net/wltom1985/article/details/54973811(该篇文章中的函数介绍的比较详细)