######################################### ###chip-seq in plant ###kuangchen 2018.9.13 ###Email:82101181029@caas.cn #installation source("https://bioconductor.org/biocLite.R") biocLite("org.At.tair.db") source("https://bioconductor.org/biocLite.R") biocLite("TxDb.Athaliana.BioMart.plantsmart28") library("ChIPseeker") library("org.At.tair.db") library("TxDb.Athaliana.BioMart.plantsmart28") library("VennDiagram") library("clusterProfiler") #输入peak.bed文件 FHY1 <- readPeakFile("F:\\研究僧\\实验研究\\CHIP\\chip-plant\\GSM1400501_FHY1_FR1.bed") FHY2 <- readPeakFile("F:\\研究僧\\实验研究\\CHIP\\chip-plant\\GSM1400502_FHY2_FR2.bed") FHY3 <- readPeakFile("F:\\研究僧\\实验研究\\CHIP\\chip-plant\\GSM1400503_FHY3_FR3.bed") print(FHY1) print(FHY2) print(FHY3) FHY1_peak <- readPeakFile(FHY1[[4]]) FHY1_peak <-readPeakFile(FHY1[[4]]) FHY2_peak <-readPeakFile(FHY2[[4]]) FHY3_peak <-readPeakFile(FHY3[[4]]) #注释 FHY1_peakAnno <-annotatePeak(FHY1,tssRegion = c(-2500,2499),TxDb = "TxDb.Athaliana.BioMart.plantsmart28", annoDb = "org.At.tair.db") FHY2_peakAnno <-annotatePeak(FHY2,tssRegion = c(-2500,2500),TxDb = "TxDb.Athaliana.BioMart.plantsmart28", annoDb = "org.At.tair.db") FHY3_peakAnno <-annotatePeak(FHY3,tssRegion = c(-2500,2500),TxDb = "TxDb.Athaliana.BioMart.plantsmart28", annoDb = "org.At.tair.db") covplot(FHY1, weightCol="V5") covplot(FHY2, weightCol="V5") covplot(FHY3, weightCol="V5") 在运行print(FHY1)，显示文件如下： > print(FHY1) GRanges object with 8423 ranges and 7 metadata columns: seqnames ranges strand | V4 V5 V6 V7 V8 V9 | [1] Chr3 14202686-14202943 * | 259 129 2340 3100 86.01 0 [2] Chr3 14200932-14201189 * | 259 129 2275 3100 83.62 0 [3] Chr2 3239786-3240043 * | 259 129 2225 3100 81.78 0 [4] Chr3 14199470-14200210 * | 742 183 5379 3100 79.19 0 [5] Chr2 3241105-3241362 * | 259 129 1925 3100 70.76 0 ... ... ... ... . ... ... ... ... ... ... [8419] Chr4 10780103-10781397 * | 1296 307 436 51.34 3.04 0.76 [8420] Chr5 4464031-4465049 * | 1020 723 301 52.07 3.04 0.76 [8421] Chr4 14597219-14598374 * | 1157 345 512 54.17 3.04 0.77 [8422] Chr3 359985-361663 * | 1680 1058 596 50.08 3.04 0.78 [8423] Chr5 26250587-26251913 * | 1328 331 418 50.53 3.04 0.78 V10 [1] 86 [2] 83.6 [3] 81.8 [4] 79.2 [5] 70.8 ... ... [8419] 3 [8420] 3 [8421] 3 [8422] 3 [8423] 3 ------- 在运行FHY1_peak <-readPeakFile(FHY1[[4]])出现报错：如下： > FHY1_peak <- readPeakFile(FHY1[[4]]) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘getListElement’ for signature ‘"GRanges"’ 在运行FHY1_peakAnno <-annotatePeak(FHY1,tssRegion = c(-2500,2499),TxDb = "TxDb.Athaliana.BioMart.plantsmart28", annoDb = "org.At.tair.db") ，出现如下报错： >> preparing features information... 2018-09-13 23:19:25 Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘metadata’ for signature ‘"character"’ 请问如何解决报错，谢谢指导