用DiffBind自带数据包做ChIP SEQ差异分析

在做完peak calling之后，我们就可以做样品间的差异分析了，常用的包是DiffBind，现在，先用自带的数据包做一个差异分析。

一、加载软件

library(DiffBind)
library(tidyverse)

二、工作路径

setwd(system.file("extra", package="DiffBind")) # 设置工作路径，在软件包DiffBind下的extra文件夹；
list.files() # 这是工作目录，其中，peaks和testdata是文件夹； 
[1] "config.csv"              "peaks"                   "tamoxifen.csv"          
[4] "tamoxifen_allfields.csv" "tamoxifen_GEO.csv"       "tamoxifen_GEO.R"        
[7] "testdata"
getwd()
[1] "C:/Users/***/Documents/R/win-library/3.6/DiffBind/extra"

三、样品信息与文件

> read.csv("tamoxifen.csv")
   SampleID Tissue Factor  Condition  Treatment Replicate                     bamReads ControlID                  bamControl
1    BT4741  BT474     ER  Resistant Full-Media         1  reads/Chr18_BT474_ER_1.bam    BT474c reads/Chr18_BT474_input.bam
2    BT4742  BT474     ER  Resistant Full-Media         2  reads/Chr18_BT474_ER_2.bam    BT474c reads/Chr18_BT474_input.bam
3     MCF71   MCF7     ER Responsive Full-Media         1   reads/Chr18_MCF7_ER_1.bam     MCF7c  reads/Chr18_MCF7_input.bam
4     MCF72   MCF7     ER Responsive Full-Media         2   reads/Chr18_MCF7_ER_2.bam     MCF7c  reads/Chr18_MCF7_input.bam
5     MCF73   MCF7     ER Responsive Full-Media         3   reads/Chr18_MCF7_ER_3.bam     MCF7c  reads/Chr18_MCF7_input.bam
6     T47D1   T47D     ER Responsive Full-Media         1   reads/Chr18_T47D_ER_1.bam     T47Dc  reads/Chr18_T47D_input.bam
7     T47D2   T47D     ER Responsive Full-Media         2   reads/Chr18_T47D_ER_2.bam     T47Dc  reads/Chr18_T47D_input.bam
8    MCF7r1   MCF7     ER  Resistant Full-Media         1   reads/Chr18_TAMR_ER_1.bam     TAMRc  reads/Chr18_TAMR_input.bam
9    MCF7r2   MCF7     ER  Resistant Full-Media         2   reads/Chr18_TAMR_ER_2.bam     TAMRc  reads/Chr18_TAMR_input.bam
10    ZR751   ZR75     ER Responsive Full-Media         1  reads/Chr18_ZR75_ER_1.bam     ZR75c  reads/Chr18_ZR75_input.bam
11    ZR752   ZR75     ER Responsive Full-Media         2  reads/Chr18_ZR75_ER_2.bam     ZR75c  reads/Chr18_ZR75_input.bam
                     Peaks PeakCaller
1  peaks/BT474_ER_1.bed.gz        bed
2  peaks/BT474_ER_2.bed.gz        bed
3   peaks/MCF7_ER_1.bed.gz        bed
4   peaks/MCF7_ER_2.bed.gz        bed
5   peaks/MCF7_ER_3.bed.gz        bed
6   peaks/T47D_ER_1.bed.gz        bed
7   peaks/T47D_ER_2.bed.gz        bed
8   peaks/TAMR_ER_1.bed.gz        bed
9   peaks/TAMR_ER_2.bed.gz        bed
10  peaks/ZR75_ER_1.bed.gz        bed
11  peaks/ZR75_ER_2.bed.gz        bed

> list.files("peaks")
 [1] "BT474_ER_1.bed.gz" "BT474_ER_2.bed.gz" "MCF7_ER_1.bed.gz" 
 [4] "MCF7_ER_2.bed.gz"  "MCF7_ER_3.bed.gz"  "T47D_ER_1.bed.gz" 
 [7] "T47D_ER_2.bed.gz"  "TAMR_ER_1.bed.gz"  "TAMR_ER_2.bed.gz" 
[10] "ZR75_ER_1.bed.gz"  "ZR75_ER_2.bed.gz"

dba函数用于创建DBA（Differential Binding Affinity）对象

> ta <- dba(sampleSheet="tamoxifen.csv")
BT4741 BT474 ER Resistant Full-Media 1 bed
BT4742 BT474 ER Resistant Full-Media 2 bed
MCF71 MCF7 ER Responsive Full-Media 1 bed
MCF72 MCF7 ER Responsive Full-Media 2 bed
MCF73 MCF7 ER Responsive Full-Media 3 bed
T47D1 T47D ER Responsive Full-Media 1 bed
T47D2 T47D ER Responsive Full-Media 2 bed
MCF7r1 MCF7 ER Resistant Full-Media 1 bed
MCF7r2 MCF7 ER Resistant Full-Media 2 bed
ZR751 ZR75 ER Responsive Full-Media 1 bed
ZR752 ZR75 ER Responsive Full-Media 2 bed

> ta
11 Samples, 2845 sites in matrix (3795 total): # 在11个样品中，总计3795个unique peaks，其中，2602个sites overlap in at least two of the samples
       ID Tissue Factor  Condition  Treatment Replicate Caller Intervals
1  BT4741  BT474     ER  Resistant Full-Media         1    bed      1080
2  BT4742  BT474     ER  Resistant Full-Media         2    bed      1122
3   MCF71   MCF7     ER Responsive Full-Media         1    bed      1556
4   MCF72   MCF7     ER Responsive Full-Media         2    bed      1046
5   MCF73   MCF7     ER Responsive Full-Media         3    bed      1339
6   T47D1   T47D     ER Responsive Full-Media         1    bed       527
7   T47D2   T47D     ER Responsive Full-Media         2    bed       373
8  MCF7r1   MCF7     ER  Resistant Full-Media         1    bed      1438
9  MCF7r2   MCF7     ER  Resistant Full-Media         2    bed       930
10  ZR751   ZR75     ER Responsive Full-Media         1    bed      2346
11  ZR752   ZR75     ER Responsive Full-Media         2    bed      2345

> names(ta)
 [1] "config"      "chrmap"      "peaks"       "class"       "masks"      
 [6] "samples"     "called"      "totalMerged" "merged"      "binding"    
[11] "attributes"  "minOverlap"