Question

我已经生成了一个表格来显示不同基因列表之间的重叠。因为我有八个不同的基因列表，所以我有64个结果。我目前拥有的代码如下：

#-------------------------------------------------------------------------------
# Set the working directory and load the data files
#-------------------------------------------------------------------------------
setwd("~/Desktop/R_Project/Gene_overlap")
getwd()
files <- list.files(pattern="*.txt", full.names = TRUE)
files

data.list <- lapply(files, function(fil) {
  scan(file=fil, what=character())
})

names(data.list) <- basename(files) %>% stringr::str_remove("\\.txt$")

str(data.list)
# List of 8
# $ GSE108363_BCGdown_D: chr [1:350] "IL1B" "IL6" "IL1A" "CCL20" ...
# $ GSE108363_BCGdown_V: chr [1:267] "IL6" "CCL20" "IL1A" "CXCL5" ...
# $ GSE108363_BCGup_D  : chr [1:250] "FABP4" "CMTM2" "FUCA1" "CD36" ...
# $ GSE108363_BCGup_V  : chr [1:429] "FCN1" "FCGR3B" "MNDA" "CPVL" ...
# $ GSE108363_MTBdown_D: chr [1:86] "CCL20" "IL1B" "IL1A" "IL6" ...
# $ GSE108363_MTBdown_V: chr [1:244] "IL1B" "IL1A" "CCL20" "IL6" ...
# $ GSE108363_MTBup_D  : chr [1:128] "FUCA1" "FGL2" "TGFBI" "CPVL" ...
# $ GSE108363_MTBup_V  : chr [1:286] "FABP4" "RNASE1" "MNDA" "CPVL" ...

intersect(data.list$GSE108363_BCGdown_D, data.list$GSE108363_BCGdown_V) %>% length

sapply(data.list, length)



#-------------------------------------------------------------------------------
# Using the intersect function to see the overlaps 
#-------------------------------------------------------------------------------

data.file1 <- "GSE108363_BCGdown_V.txt"
data.file2 <- "GSE108363_BCGdown_D.txt"
data.file3 <- "GSE108363_BCGup_V.txt"
data.file4 <- "GSE108363_BCGup_D.txt"
data.file5 <- "GSE108363_MTBdown_V.txt"
data.file6 <- "GSE108363_MTBdown_D.txt"
data.file7 <- "GSE108363_MTBup_V.txt"
data.file8 <- "GSE108363_MTBup_D.txt"

genevect1 <- scan(data.file1, what=character(), sep="\n")
genevect2 <- scan(data.file2, what=character(), sep="\n")
genevect3 <- scan(data.file3, what=character(), sep="\n")
genevect4 <- scan(data.file4, what=character(), sep="\n")
genevect5 <- scan(data.file5, what=character(), sep="\n")
genevect6 <- scan(data.file6, what=character(), sep="\n")
genevect7 <- scan(data.file7, what=character(), sep="\n")
genevect8 <- scan(data.file8, what=character(), sep="\n")


filelist <- list(data.file1, data.file2, data.file3, data.file4, data.file5, data.file6, data.file7, data.file8)
all(sapply(filelist, file.exists))

# read files:
gene.lists <- lapply(filelist, function(f) {
  scan(file=f, what=character())
})


# set up empty matrix
x <- (length(gene.lists))^2
x
y <- rep(NA, x)
mx <- matrix(y, ncol=length(gene.lists))
mx
row.names(mx) <- sapply(filelist, basename) %>% stringr::str_remove('.txt$')
colnames(mx) <- sapply(filelist, basename) %>% stringr::str_remove('.txt$')
mx

mx.overlap.count <- mx

# seq_along(gene.lists) # 1 2 3 4 5 6 7 8
for (i in seq_along(gene.lists)) {
  g1 <- gene.lists[[i]]
  for (j in seq_along(gene.lists)) {
    g2 <- gene.lists[[j]]
    a <- intersect(g1, g2)
    b <- length(a)
    mx.overlap.count[j,i] <- b
  }
}

mx.overlap.count
View(mx.overlap.count)

我现在想做类似的事情，但我不想看到重叠的数字，而是想看到不同基因列表之间的重叠程度百分比。我将需要以某种方式查看g1或g2是否更大，以便在乘以100之前将b除以更大的整数。任何建议将不胜感激。

Answer 1

使用字母样本，因为您没有提供基因列表：

set.seed(1)
data.list <- lapply(sample(10:20), function(n)LETTERS[sample(1:26, n)])

overlaps <- sapply(data.list, function(g1) 
  sapply(data.list, function(g2)
  {round(length(intersect(g1, g2)) / length(g2) * 100)}))

overlaps
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
 [1,]  100   50   67   75   42   92   58   92   67    33    92
 [2,]   46  100   62   69   54   77   62   69   69    54    62
 [3,]   53   53  100   60   33   73   60   73   80    33    60
 [4,]   53   53   53  100   47   71   53   76   53    29    82
 [5,]   45   64   45   73  100   91   64   82   36    45    73
 [6,]   61   56   61   67   56  100   56   89   56    33    72
 [7,]   50   57   64   64   50   71  100   86   71    50    64
 [8,]   55   45   55   65   45   80   60  100   60    40    80
 [9,]   50   56   75   56   25   62   62   75  100    38    69
[10,]   40   70   50   50   50   60   70   80   60   100    70
[11,]   58   42   47   74   42   68   47   84   58    37   100

（我使用了set.seed，所以您可以重现该示例）。它使用嵌套的sapply分别遍历两个基因列表，然后通过将相交的长度除以第二个基因载体的总长度来计算每个基因载体组合的百分比。如果要除以2个基因载体中最长的一个的长度，请将length(g2)替换为max(length(g1), length(g2))

计算不同基因列表之间的基因重叠百分比

1 个答案: