dandanwu90
2019年4月11日
不自我檢測怎么知道我什么都不會谷饿？
把我盤倒的R語言中級10個題目在這里拼坎。
Q1:
根據(jù)R包org.Hs.eg.db找到下面ensembl 基因ID 對應(yīng)的基因名(symbol)
ENSG00000000003.13
ENSG00000000005.5
ENSG00000000419.11
ENSG00000000457.12
ENSG00000000460.15
ENSG00000000938.11
提示：
library(org.Hs.eg.db)
g2s=toTable(org.Hs.egSYMBOL)
g2e=toTable(org.Hs.egENSEMBL)
suppressMessages(library(org.Hs.eg.db))
#查看包里面的內(nèi)容
keytypes(org.Hs.eg.db)
columns(org.Hs.eg.db)
g2s=toTable(org.Hs.egSYMBOL)
g2e=toTable(org.Hs.egENSEMBL)
head(g2s)
head(g2e)
ensembl_id=c("ENSG00000000003.13", "ENSG00000000005.5","ENSG00000000419.11","ENSG00000000457.12","ENSG00000000460.15","ENSG00000000938.11")
ensembl_id=as.data.frame(ensembl_id)
library(stringr)
ensembl_id=str_split(ensembl_id$ensembl_id,pattern ="[.]",simplify = T)[,1]
ensembl_id=as.data.frame(ensembl_id)
b=merge(ensembl_id,g2e,by='ensembl_id',all.x=T)
d=merge(b,g2s,by="gene_id",all.x=T)
Q2:
根據(jù)R包hgu133a.db找到下面探針對應(yīng)的基因名(symbol)
1053_at
117_at
121_at
1255_g_at
1316_at
1320_at
1405_i_at
1431_at
1438_at
1487_at
1494_f_at
1598_g_at
160020_at
1729_at
177_at
提示：
library(hgu133a.db)
ids=toTable(hgu133aSYMBOL)
head(ids)
suppressMessages(library(hgu133a.db))
keytypes(hgu133a.db)
ids=toTable(hgu133aSYMBOL)
a=read.csv(file='probe_id',header = F)
colnames(a)='probe_id'
mydata=merge(a,ids,by="probe_id",all.x=T)
Q3:
找到R包CLL內(nèi)置的數(shù)據(jù)集的表達(dá)矩陣?yán)锩娴腡P53基因的表達(dá)量亏狰，并且繪制在 progres.-stable分組的boxplot圖
提示：
suppressPackageStartupMessages(library(CLL))
data(sCLLex)
sCLLex
exprSet=exprs(sCLLex)
library(hgu95av2.db)
想想如何通過 ggpubr 進(jìn)行美化稽犁。
suppressPackageStartupMessages(library(CLL))
data("sCLLex")
exprSet=as.data.frame(exprs(sCLLex))
pd=pData(sCLLex)
library(hgu95av2.db)
keytypes(hgu95av2.db)
gene2s=toTable(hgu95av2SYMBOL)
gene2s_filter=gene2s[gene2s$symbol=='TP53',]
exprSet$probe_id=rownames(exprSet)
exprSet2_filter=merge(gene2s_filter,exprSet,by='probe_id',all.x=T)
rownames(exprSet2_filter)=exprSet2_filter[,1]
exprSet2_filter=exprSet2_filter[,c(-1,-2)]
exprSet2_filter=as.data.frame(t(exprSet2_filter))
exprSet2_filter$Disease=pd$Disease
library(reshape)
exprSet2=melt(exprSet2_filter,id='Disease')
library(ggplot2)
ggplot(exprSet2, aes(x=variable, y=value, fill = Disease))+
geom_boxplot(position=position_dodge(1))+
geom_dotplot(binaxis='y', stackdir='center',
position=position_dodge(1),binwidth =0.05)
Q4:
找到BRCA1基因在TCGA數(shù)據(jù)庫的乳腺癌數(shù)據(jù)集(Breast Invasive Carcinoma (TCGA, PanCancer Atlas))的表達(dá)情況
提示：
使用http://www.cbioportal.org/index.do 定位數(shù)據(jù)集：http://www.cbioportal.org/datasets
a=read.csv(file='plot4.txt',sep="\t",header = T)
colnames(a)
colnames(a)=c("id","subtype","expression","mutant")
library("ggstatsplot")
ggbetweenstats(
data = a,
x = 'subtype',
y = 'expression')
library("ggpubr")
ggboxplot(data =a, x = 'subtype', y = 'expression',
color = "subtype",
add = "jitter", shape = "subtype")
數(shù)據(jù)網(wǎng)址在這里
步驟如下：Q4_1, Q4_2
Q5:
找到TP53基因在TCGA數(shù)據(jù)庫的乳腺癌數(shù)據(jù)集的表達(dá)量分組看其是否影響生存
BRCA_7157_10_80=read.csv(file ='BRCA_7157_10_80.csv',header = T )
colnames(BRCA_7157_10_80)
library(ggstatsplot)
ggbetweenstats(
data = BRCA_7157_10_80,
x = 'Status',
y = 'Expression')
數(shù)據(jù)網(wǎng)址在這里
步驟如下：Q5_1,Q5_2
Q6:
下載數(shù)據(jù)集GSE17215的表達(dá)矩陣并且提取下面的基因畫熱圖
ACTR3B ANLN BAG1 BCL2 BIRC5 BLVRA CCNB1 CCNE1 CDC20 CDC6 CDCA1 CDH3 CENPF CEP55 CXXC5 EGFR ERBB2 ESR1 EXO1 FGFR4 FOXA1 FOXC1 GPR160 GRB7 KIF2C KNTC2 KRT14 KRT17 KRT5 MAPT MDM2 MELK MIA MKI67 MLPH MMP11 MYBL2 MYC NAT1 ORC6L PGR PHGDH PTTG1 RRM2 SFRP1 SLC39A6 TMEM45B TYMS UBE2C UBE2T
提示：
根據(jù)基因名拿到探針I(yè)D熔号，縮小表達(dá)矩陣?yán)L制熱圖翎冲，沒有檢查到的基因直接忽略即可绊率。
suppressMessages(library(GEOquery))
Q6=getGEO("GSE17215",AnnotGPL = F,getGPL = F)
show(Q6)
Series_m=Q6$GSE17215_series_matrix.txt.gz
Series_m=as.data.frame(exprs(Series_m))
head(Series_m)
dim(Series_m)
suppressMessages(library(hgu133a.db))
keytypes(hgu133a.db)
ids=toTable(hgu133aSYMBOL)
#加戲疑問：如果不過濾沒有檢測到的基因谨敛，那么統(tǒng)計有多少個基因沒有檢測到
Q6_gene=read.csv(file="Q6.txt",sep="\t",header = F)
colnames(Q6_gene)="symbol"
Q6_mydata=merge(Q6_gene,ids,by="symbol")
Series_m$probe_id=rownames(Series_m)
Series_m_filter=merge(Q6_mydata,Series_m,by="probe_id")
rownames(Series_m_filter)=Series_m_filter[,1]
Series_m_filter=Series_m_filter[,c(-1,-2)]
library(pheatmap)
n=t(scale(t( Series_m_filter ))) #scale()函數(shù)去中心化和標(biāo)準(zhǔn)化
#對每個探針的表達(dá)量進(jìn)行去中心化和標(biāo)準(zhǔn)化
n[n>2]=2 #矩陣n中歸一化后，大于2的項滤否，賦值使之等于2（相當(dāng)于設(shè)置了一個上限）
n[n< -2]= -2 #小于-2的項脸狸，賦值使之等于-2（相當(dāng)于設(shè)置了一個下限）
n[1:4,1:4]
pheatmap(n,show_rownames=F,clustering_distance_rows = "correlation")
Q7:
下載數(shù)據(jù)集GSE24673的表達(dá)矩陣計算樣本的相關(guān)性并且繪制熱圖，需要標(biāo)記上樣本分組信息
suppressMessages(library(GEOquery))
Q7=getGEO("GSE24673",AnnotGPL = F,getGPL = F)
show(Q7)
Q7_m=Q7$GSE24673_series_matrix.txt.gz
Q7_exprs=as.data.frame(exprs(Q7_m))
head(Q7_exprs)
dim(Q7_exprs)
Q7_pd=pData(Q7_m)
Q7_group=Q7_pd[,"source_name_ch1"]
Q7_group=as.data.frame(Q7_group,row.names = rownames(Q7_pd))
colnames(Q7_group)="group_list"
library(pheatmap)
pheatmap(Q7_exprs,scale = 'row', show_rownames=F,annotation_col = Q7_group)
Q8:
找到 GPL6244 platform of Affymetrix Human Gene 1.0 ST Array 對應(yīng)的R的bioconductor注釋包藐俺，并且安裝它炊甲！
options()
BioC_mirror
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
BiocManager::install("請輸入自己找到的R包",ask = F,update = F)
options()
hugene10sttranscriptcluster
BiocManager::install("hugene10sttranscriptcluster.db")
Q9:
下載數(shù)據(jù)集GSE42872的表達(dá)矩陣，并且分別挑選出 所有樣本的(平均表達(dá)量/sd/mad/)最大的探針欲芹，并且找到它們對應(yīng)的基因
suppressMessages(library(GEOquery))
Q9=getGEO("GSE42872",AnnotGPL = F,getGPL = F)
show(Q9)
Q9_m=Q9$GSE42872_series_matrix.txt.gz
Q9_exprs=as.data.frame(exprs(Q9_m))
head(Q9_exprs)
dim(Q9_exprs)
sort(apply(Q9_exprs,1,mean),decreasing = T)[1]
# 7978905
# 14.53288
sort(apply(Q9_exprs,1,sd),decreasing = T)[1]
# 8133876
# 3.166429
sort(apply(Q9_exprs,1,mad),decreasing = T)[1]
# 8133876
# 4.268561
suppressMessages(library("hugene10sttranscriptcluster.db"))
keytypes(hugene10sttranscriptcluster.db)
Q9_ids=toTable(hugene10sttranscriptclusterSYMBOL)
Q9_mean_g2s=Q9_ids[Q9_ids$probe_id%in%7978905,]
#沒找到
Q9_sd_g2s=Q9_ids[Q9_ids$probe_id%in%8133876,]
#CD36
Q10:
下載數(shù)據(jù)集GSE42872的表達(dá)矩陣卿啡，并且根據(jù)分組使用limma做差異分析，得到差異結(jié)果矩陣
#與Q9數(shù)據(jù)一致菱父，故不改數(shù)據(jù)名稱
suppressMessages(library(GEOquery))
Q9=getGEO("GSE42872",AnnotGPL = F,getGPL = F)
show(Q9)
Q9_m=Q9$GSE42872_series_matrix.txt.gz
Q9_exprs=as.data.frame(exprs(Q9_m))
head(Q9_exprs)
dim(Q9_exprs)
Q9_pd=pData(Q9_m)
Q9_group=Q9_pd[,"source_name_ch1"]
Q9_group=as.data.frame(Q9_group,row.names = rownames(Q9_pd))
colnames(Q9_group)="group_list"
library("stringr")
Q9_group_list=as.data.frame(str_split(Q9_group$group_list,pattern = " ",simplify = T)[,6],row.names = rownames(Q9_group))
colnames(Q9_group_list)="group_list"
suppressMessages(library(limma))
design=model.matrix(~0+factor(Q9_group_list$group_list))
colnames(design)=c("vehicle","vemurafenib")
rownames(design)=rownames(Q9_group_list)
design
contrast.matrix=makeContrasts("vehicle-vemurafenib",levels = design)
contrast.matrix
fit=lmFit(Q9_exprs,design)
fit2=contrasts.fit(fit,contrast.matrix)
fit2=eBayes(fit2)
temOutput=topTable(fit2,coef = 1,n=Inf)
nrDEG=na.omit(temOutput)
head(nrDEG)
#加戲日常颈娜，差異分析都出來了，怎么不畫個圖浙宜？火山圖來了
logFC_Cutof=with(nrDEG,mean(abs( logFC)) + 2*sd(abs( logFC)))
logFC_Cutof=0
nrDEG$change=as.factor(ifelse(nrDEG$P.Value<0.01 & abs(nrDEG$logFC)>logFC_Cutof,
ifelse(nrDEG$logFC>logFC_Cutof,'UP','DOWN'),'NOT'))
this_tile <- paste0('Cutoff for logFC is ',round(logFC_Cutof,3),'\nThe number of up gene is ',nrow(nrDEG[nrDEG$change =='UP',]) ,'\nThe number of down gene is ',nrow(nrDEG[nrDEG$change =='DOWN',]))
library(ggplot2)
g_volcano=ggplot(data=nrDEG,aes(x=logFC, y=-log10(P.Value),color=change))+
geom_point(alpha=0.4, size=1.75)+
theme_set(theme_set(theme_bw(base_size=20)))+
xlab("log2 fold change") + ylab("-log10 p-value") +
ggtitle( this_tile ) +
theme(plot.title = element_text(size=15,hjust = 0.5))+
scale_colour_manual(values = c('blue','black','red'))
print(g_volcano)
做完題了
