我正在尝试在数据中建立一个共现矩阵。我有141行和544列的数据框。每列包含0和1。数据集示例：
OTU_1 OTU_10 OTU_100 OTU_101 OTU_109
1 1 1 0 0
1 1 0 0 1
1 1 0 0 0
1 1 1 1 1
1 1 1 1 1
我的数据的原始结构：
data.frame': 141 obs. of 544 variables:
$ OTU_1 : Factor w/ 1 level "1": 1 1 1 1 1 1 1 1 1 1 ...
$ OTU_10 : Factor w/ 2 levels "0","1": 2 2 2 2 2 2 2 2 2 2 ...
$ OTU_100 : Factor w/ 2 levels "0","1": 2 1 1 2 2 2 1 2 2 2 ...
现在，我想一次将一列与其他列和另一行进行比较。因此，我尝试了以下代码：
gen.cyscd_df <- function(x){
help.df <- data.frame(otu1 = row.names(x)[1] , otu2 = rownames(x), counts= 0)
for (i in 1:ncol(x)){
help.df <- rbind.data.frame(help.df, data.frame(otu1 = col.names(x)[i] ,
otu2 = col.names(x)[i:length(colnames(x))],
counts= 0))
}
row.names(help.df) <- NULL
return(help.df)
}
single.otu.df <- gen.cyscd_df(bin_OTU_tab)
以上代码的str为：
data.frame': 91961 obs. of 3 variables:
$ otu1 : Factor w/ 141 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 1 1 ...
$ otu2 : Factor w/ 141 levels "1","10","100",..: 1 54 65 76 87 98 109 120 131 2 ...
$ counts: num 0 0 0 0 0 0 0 0 0 0 ...
下一步是根据1个OTU与其他OTU的共存替换列数
single.otu.matrix_row <- function(x){
single.otu.df2 <- single.otu.df
for (otu1 in 1:nrow(x)){
for(otu2 in 1:nrow(x)){
if(x[otu1,1] ==1 && x[otu2,1] ==1) {
single.otu.df[otu1+otu2] <- 1}
}
}
return(single.otu.df2)
}
x<-single.otu.matrix_row(as.matrix(bin_OTU_tab[1:nrow(bin_OTU_tab),1]))
但是在counts列中，我无法替换0值。
data.frame': 91961 obs. of 3 variables:
$ otu1 : Factor w/ 141 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 1 1 ...
$ otu2 : Factor w/ 141 levels "1","10","100",..: 1 54 65 76 87 98 109 120 131 2 ...
$ counts: num 0 0 0 0 0 0 0 0 0 0 ...
但是预期的输出是（对于第一行）
OTU1 OTU2 Counts
1 10 1
1 100 1
1 101 0
1 109 0
我哪里出错了。请指导我