大神一句話，菜鳥(niǎo)跑半年。我不是大神，但我可以縮短你走彎路的半年~ 就像歌兒唱的那樣,，如果你不知道該往哪兒走,，就留在這學(xué)點(diǎn)生信好不好~ 這里有豆豆和花花的學(xué)習(xí)歷程,，從新手到進(jìn)階,，生信路上有你有我,！ 大年初六，加油油,。 本文題目出自生信技能樹(shù)R語(yǔ)言學(xué)習(xí)視頻,，文末有鏈接：從CLL內(nèi)置數(shù)據(jù)集的表達(dá)矩陣中找TP53基因的表達(dá)量
rm(list=ls())
options(stringsAsFactors = F)
if(!suppressMessages(require('hgu95av2.db')))BiocManager::install('hgu95av2.db')
if(!suppressMessages(require('CLL')))BiocManager::install('CLL')
if(!suppressMessages(require(tidyverse)))install.packages('tidyverse')
if(!suppressMessages(require(ggpubr)))install.packages('ggpubr')
suppressMessages(library(hgu95av2.db))
suppressMessages(library(CLL))
suppressMessages(library(ggpubr))
data(sCLLex)
# sCLLex
exprSet <>#探針的表達(dá)量
exprSet[1:4,1:4]
#> CLL11.CEL CLL12.CEL CLL13.CEL CLL14.CEL
#> 1000_at 5.743132 6.219412 5.523328 5.340477
#> 1001_at 2.285143 2.291229 2.287986 2.295313
#> 1002_f_at 3.309294 3.318466 3.354423 3.327130
#> 1003_s_at 1.085264 1.117288 1.084010 1.103217
pd <>#sampleID與disease的對(duì)應(yīng)關(guān)系
head(pd)
#> SampleID Disease
#> CLL11.CEL CLL11 progres.
#> CLL12.CEL CLL12 stable
#> CLL13.CEL CLL13 progres.
#> CLL14.CEL CLL14 progres.
#> CLL15.CEL CLL15 progres.
#> CLL16.CEL CLL16 progres.
p2s <>#探針與symbol的對(duì)應(yīng)關(guān)系
head(p2s)
#> probe_id symbol
#> 1 1000_at MAPK3
#> 2 1001_at TIE1
#> 3 1002_f_at CYP2C19
#> 4 1003_s_at CXCR5
#> 5 1004_at CXCR5
#> 6 1005_at DUSP1
p3 <>'TP53')
# boxplot [find TP53 has 3 probe IDs]
probe_tp53 <>
for(i in 1:3){
boxplot(exprSet[probe_tp53[i],] ~ pd$Disease)
}
   #用ggpubr作圖
#http://www./english/articles/24-ggpubr-publication-ready-p#lots/
expd <>
expd[1:4,1:4]
#> rowname CLL11.CEL CLL12.CEL CLL13.CEL
#> 1 1000_at 5.743132 6.219412 5.523328
#> 2 1001_at 2.285143 2.291229 2.287986
#> 3 1002_f_at 3.309294 3.318466 3.354423
#> 4 1003_s_at 1.085264 1.117288 1.084010
expd2 <>
key = 'sample',
value = 'exp',-1)
pd <>
head(pd)
#> rowname SampleID Disease
#> 1 CLL11.CEL CLL11 progres.
#> 2 CLL12.CEL CLL12 stable
#> 3 CLL13.CEL CLL13 progres.
#> 4 CLL14.CEL CLL14 progres.
#> 5 CLL15.CEL CLL15 progres.
#> 6 CLL16.CEL CLL16 progres.
expd3 <>'sample'='rowname'))
i=1 ###可換1，2
for(i in 1:3){
p <>
x = 'Disease',
y = 'exp',
color = 'Disease', palette =c('#00AFBB', '#E7B800', '#FC4E07'),
add = 'jitter', shape = 'Disease')
print(p)
}
|
