我正在按照Rhea脚本分析微生物测序数据。最后一个命令给我错误说＆＃34;
参数1不是向量
虽然我已经密切关注了剧本。
查找下面附带的会话信息。
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> setwd("C:/Users/Jonas/Desktop/Bielefeld")
> file_name<- "C:/Users/Jonas/Desktop/Bielefeld/OTUs_Table-norm.tab"
> Species.richness <- function(x)
+ {
+
+ count=sum(x[x>0.5]^0)
+ return(count)
+ }
> Shannon.entropy <- function(x)
+ {
+ total=sum(x)
+ se=-sum(x[x>0]/total*log(x[x>0]/total))
+ return(se)
+ }
> Shannon.effective <- function(x)
+ {
+ total=sum(x)
+ se=round(exp(-sum(x[x>0]/total*log(x[x>0]/total))),digits =2)
+ return(se)
+ }
> Simpson.concentration <- function(x)
+ {
+ total=sum(x)
+ si=sum((x[x>0]/total)^2)
+ return(si)
+ }
> Simpson.effective <- function(x)
+ {
+ total=sum(x)
+ si=round(1/sum((x[x>0]/total)^2),digits =2)
+ return(si)
+ }
> otu_table <- read.table (file_name,
+ check.names = FALSE,
+ header=TRUE,
+ dec=".",
+ sep = "\t",
+ row.names = 1)
> otu_table <- otu_table[!apply(is.na(otu_table) | otu_table=="",1,all),]
>
> my_otu_table <- otu_table[,order(names(otu_table))]
Error in order(names(otu_table)) : argument 1 is not a vector
> my_otu_table <-data.frame(t(my_otu_table))
Error in t(my_otu_table) : object 'my_otu_table' not found`
'> str(otu_table)
'data.frame': 166 obs. of 1 variable:
$ Sample1: int 102243 48415 5602 9142 1560 1099 1153 1088 1891 414 ...
> otu_table <- otu_table[!apply(is.na(otu_table) | otu_table=="",1,all),]
>
> str(otu_table)
int [1:166] 102243 48415 5602 9142 1560 1099 1153 1088 1891 414 ...
>
> otu_table[!is.na(otu_table)]
[1] 102243 48415 5602 9142 1560 1099 1153 1088 1891 414
526 504 612 795 568
[16] 459 680 212 207 265 156 149 149 228 327
212 114 666 296 751
[31] 37 272 220 851 126 162 250 122 124 431
118 221 141 153 83
[46] 51 149 256 166 120 158 11 116 84 291
130 371 138 129 58
[61] 98 176 86 69 192 27 59 31 61 35
58 110 46 105 153
[76] 87 6 119 31 100 84 61 9 60 201
101 68 4 439 46
[91] 59 35 61 97 11 16 167 101 46 127
16 101 144 8 65
[106] 55 51 39 48 6 93 2 2 37 24
15 15 24 52 3
[121] 2 2 27 13 2 2 131 10 32 5
49 41 2 56 83
[136] 2 11 77 75 20 5 33 95 57 4
7 24 57 27 19
[151] 55 2 4 693 15 2 3 12 19 8
4 108 72 12 5
[166] 2
> my_otu_table <- otu_table[order(names(otu_table))]
Error in order(names(otu_table)) : argument 1 is not a vector
> my_otu_table <-data.frame(t(my_otu_table))
Error in t(my_otu_table) : object 'my_otu_table' not found'