提取水稻promoter的坐标并转换成为bed文件

数据来源于ngsplot的MSU的基因组文件

load("F:/H3K9hib_salt/WT_chip-seq/Meta_plots/MSUv7.ensembl.exon.promoter.protein_coding.RData")

# 检查对象的类型
class(genome.coord)

# 尝试将对象转换为数据框
if (class(genome.coord) != "data.frame") {
  genome.coord <- as.data.frame(genome.coord)
  print("The object has been converted to a data frame.")
} else {
  print("The object is already a data frame.")
}

# 查看转换后的数据框内容
head(genome.coord)

 chrom start   end                   gid                 gname                   tid strand    class        biotype byname.uniq bygid.uniq
75652  ChrSy   785  1168  ChrSy.fgenesh.gene.1  ChrSy.fgenesh.gene.1  ChrSy.fgenesh.mRNA.1      - promoter protein_coding        TRUE       TRUE
329717 ChrSy 50779 51012 ChrSy.fgenesh.gene.10 ChrSy.fgenesh.gene.10 ChrSy.fgenesh.mRNA.10      - promoter protein_coding        TRUE       TRUE
337755 ChrSy 53593 53841 ChrSy.fgenesh.gene.11 ChrSy.fgenesh.gene.11 ChrSy.fgenesh.mRNA.11      - promoter protein_coding        TRUE       TRUE
325371 ChrSy 58993 59748 ChrSy.fgenesh.gene.12 ChrSy.fgenesh.gene.12 ChrSy.fgenesh.mRNA.12      + promoter protein_coding        TRUE       TRUE
93954  ChrSy 68366 68668 ChrSy.fgenesh.gene.13 ChrSy.fgenesh.gene.13 ChrSy.fgenesh.mRNA.13      - promoter protein_coding        TRUE       TRUE
152362 ChrSy 73936 74597 ChrSy.fgenesh.gene.14 ChrSy.fgenesh.gene.14 ChrSy.fgenesh.mRNA.14      + promoter protein_coding        TRUE       TRUE

转化为bed文件

bed_data <- genome.coord[, c("chrom", "start", "end", "gid", "strand")]

# 确保列名符合 BED 文件格式
colnames(bed_data) <- c("chrom", "chromStart", "chromEnd", "name", "strand")

# 查看转换后的数据框内容
head(bed_data)

      chrom    chromStart chromEnd        name           strand
75652  ChrSy        785     1168  ChrSy.fgenesh.gene.1      -
329717 ChrSy      50779    51012 ChrSy.fgenesh.gene.10      -
337755 ChrSy      53593    53841 ChrSy.fgenesh.gene.11      -
325371 ChrSy      58993    59748 ChrSy.fgenesh.gene.12      +
93954  ChrSy      68366    68668 ChrSy.fgenesh.gene.13      -
152362 ChrSy      73936    74597 ChrSy.fgenesh.gene.14      +


# 保存为 BED 文件
write.table(bed_data, file = "output_with_gene_id_and_strand.bed", quote = FALSE, sep = "\t", row.names = FALSE, col.names = FALSE)

print("The BED file has been saved as 'output_with_gene_id_and_strand.bed'.")