Question

我有两个文件，一个包含特定的染色体位置，另一个包含gene_name和基因的起始范围。我必须通过匹配基因的起始位置到染色体位置来找到基因名称。我的第一个文件的格式如下所示 Chromosome Position 1 394 1 447 2 534

我的第二个文件的格式是：

gene_name  chromoome  start  end
   pqr         1       201   230
   sbc         1       300   450
   ffg         2       500   550

我尝试过以下代码

setwd('/home/R/')
data = read.table(file='outfile.tsv', fill = TRUE)
data1 = read.table(file='Sample.tsv')
chr = data1[,1]
pos = data1[,2]
gene = data[,1]
beg = data[,3]
end = data[,4]

pos_sz = dim.data.frame(pos)
beg_sz = dim.data.frame(beg)
end_sz = dim.data.frame(end)

for (i in 1:length(pos))
{
pos_1 = pos[i]
x = pos_1>=beg & pos_1<=end
print(x)
if(any(x == "TRUE"))
{
t=pos[i]
print(t)
s = which(pos == t)
print(s)
v= chr[s]
print(v)
}
y=which(c(x))
print(y)
z=gene[y]
print(z)
}

我希望结果格式低于

gene_name   Chromosome   #chromosome against position
sbc              1
sbc              1
ffg              2

任何帮助都是适当的

Answer 1

您可以尝试使用func cleanUp() { let maximumDays = 10.0 let minimumDate = Date().addingTimeInterval(-maximumDays*24*60*60) func meetsRequirement(date: Date) -> Bool { return date < minimumDate } func meetsRequirement(name: String) -> Bool { return name.hasPrefix(applicationName) && name.hasSuffix("log") } do { let manager = FileManager.default let documentDirUrl = try manager.url(for: .documentDirectory, in: .userDomainMask, appropriateFor: nil, create: false) if manager.changeCurrentDirectoryPath(documentDirUrl.path) { for file in try manager.contentsOfDirectory(atPath: ".") { let creationDate = try manager.attributesOfItem(atPath: file)[FileAttributeKey.creationDate] as! Date if meetsRequirement(name: file) && meetsRequirement(date: creationDate) { try manager.removeItem(atPath: file) } } } } catch { print("Cannot cleanup the old files: \(error)") } }包

GenomicRanges

或者通过合并

library(GenomicRanges)
# data
target <- read.table(text="gene_name  chromoome  start  end
   pqr         1       201   230
   sbc         1       300   450
   ffg         2       500   550", header=T)

# set up GRange objects
d <- GRanges(c(1,1,2), IRanges(c(394,447,534), width=1))
target_range <- GRanges(target$chromoome, IRanges(start=target$start, end=target$end))

# get overlaps
OL <- findOverlaps(d, target_range)
target[as.data.frame(OL)[,2],]
    gene_name chromoome start end
2         sbc         1   300 450
2.1       sbc         1   300 450
3         ffg         2   500 550

R中基因范围中的染色体位置

1 个答案: