Question

我有一个包含函数的R脚本，我在这个问题的答案中收到了这个函数：R: For loop nested in for loop。

脚本在我的数据集的第一部分工作正常，但我现在正试图在另一部分上使用它，据我所知，它具有与第一部分完全相同的格式，但对于某些部分我在尝试使用脚本时遇到错误的原因。我无法弄清楚是什么导致错误。

这是我正在使用的脚本：

require(data.table)

MappingTable_Calibrated = read.csv2(file.choose(), header=TRUE)
head(MappingTable_Calibrated)

#The data is sorted primarily after Scaffold number in ascending order, and secondarily after Cal_Startgen in ascending order.

MappingTable_Calibratedord = MappingTable_Calibrated[order(MappingTable_Calibrated$Scaffold, MappingTable_Calibrated$Cal_Startgen),]
head(MappingTable_Calibratedord)

dt <- data.table(MappingTable_Calibratedord, key = "Scaffold,Cal_Startgen")
head(dt)

# The following function creates pairs of loci for each scaffold.
# The function is a modified version of a function found retrieved from http://www.stackoverflow.com

fn = function（dtIn，id）{

# Creates the object dtHead containing as many lines as in dtIn minus the last line)

dtHead = head(dtIn, n = nrow(dtIn) - 1)     

# The names of dtHead are appended with _a. paste0 short for: paste(x, sep="")

setnames(dtHead, paste0(colnames(dtHead), "_a")) 

# Creates the object dtTail containing as many lines as in dtIn minus the first line)

dtTail = tail(dtIn, n = nrow(dtIn) - 1)     

# The names of dtTail are appended with _b.

setnames(dtTail, paste0(colnames(dtTail), "_b")) 

# dtHead and dtTail are combined. Scaffold is defined as id. The blank column "Pairwise_Distance is added to the table.

cbind(dtHead, dtTail, Scaffold = id, Pairwise_Distance = 0) 

}

#The function is run on the data. .SDcols defines the rows to be included in the output.

output = dt[, fn(.SD, Scaffold), by = Scaffold, .SDcols = c("Name", "Startpos", "Endpos", "Rev", "Startgen", "Endgen", "Cal_Startgen", "Cal_Endgen", "Length")]
output = as.data.frame(output[, with = FALSE])

但是当试图创造＆＃34;输出＆＃34;我收到以下错误： Error in data.table(..., key = key(..1)) : Item 1 has no length. Provide at least one item (such as NA, NA_integer_etc) to be repeated to match the 2 rows in the longest column. Or, all columns can be 0 length, for insert()ing rows into.

dt看起来像这样：

Name          Length Startpos Endpos Scaffold Startgen Endgen Rev Match Cal_Startgen Cal_Endgen
1: Locus_7173    144        0    144       34   101196 101340   1     1       101196     101340
2: Locus_133     110        0    110       34   223659 223776   1     1       223659     223776
3: Locus_2746    161        0     89       65   101415 101504   1     1       101415     101576

完全输入＆＃34; dt＆＃34;可在此处找到：https://www.dropbox.com/sh/3j4i04s2rg6b63h/AADkWG3OcsutTiSsyTl8L2Vda?dl=0

Answer 1

首先跟踪导致错误的数据：

function(dtIn, id){
    dtHead = head(dtIn, n = nrow(dtIn) - 1)     
    setnames(dtHead, paste0(colnames(dtHead), "_a")) 
    dtTail = tail(dtIn, n = nrow(dtIn) - 1)     
    setnames(dtTail, paste0(colnames(dtTail), "_b")) 
    r <- tryCatch(cbind(dtHead, dtTail, Scaffold = id, Pairwise_Distance = 0), error = function(e) NULL)
    if(is.null(r)) browser()
    r
}

然后你可以看到你正在尝试cbind不同nrow / length的元素：

Browse[1]> dtHead
Empty data.table (0 rows) of 9 cols: Name_a,Startpos_a,Endpos_a,Rev_a,Startgen_a,Endgen_a...
Browse[1]> dtTail
Empty data.table (0 rows) of 9 cols: Name_b,Startpos_b,Endpos_b,Rev_b,Startgen_b,Endgen_b...
Browse[1]> id
[1] 76
Browse[1]> 0
[1] 0

不允许这样做我建议添加if(nrow(或类似内容，然后为nrow = 0个案例添加列id = integer(), Pairwise_Distance = numeric()。

数据表出错：项目没有长度？ - R.

1 个答案: