rowSums(tbl.external.all) 中的错误：“x”必须是数字

编程问答 2022-04-28

问题描述

我尝试运行 SKAT 派生的 R 工具，但遇到了一些错误。 几乎运行脚本的最后一步时

re<-iECAT.SSD.All(EC.INFO,obj=obj,method="optimal")

我收到以下错误：

Error in rowSums(tbl.external.all) : 'x' must be numeric
In addition: Warning messages:
1: Error to run iECAT for 1:1918090: Error in rowSums(tbl.external.all) : 'x' must be numeric

2: In if (class(try1) != "try-error") { :
  the condition has length > 1 and only the first element will be used
3: No polymorphic SNPs!
4: In if (class(try1) != "try-error") { :
  the condition has length > 1 and only the first element will be used

以前的函数和对象分配没有问题。 以下是我在 R 脚本中运行的命令行：

library(SKAT)
library(MetaSKAT)
library(iECAT)
File.bed<-"file.bed"
File.Bim<-"file.bim"
File.Fam<-"fam_all.fam"
File.SetID<-"file.setID"
File.EC<-("file.txt")
File.SSD<-"file.SSD"
File.Info<-"file.SSD.INFO"
File.EC.Info<-"file.SSD.ECINFO"
FAM<-Read_Plink_FAM(File.Fam,Is.binary=TRUE)
Generate_SSD_SetID_wEC(File.bed,File.Bim,File.Fam,File.SetID,File.EC,File.SSD,File.Info,File.EC.Info)

EC.INFO= Open_SSD_wEC(File.SSD,File.EC.Info)

obj<-SKAT_Null_Model(Phenotype ~ 1,out_type="D",data=FAM)
re<-iECAT.SSD.All(EC.INFO,method="optimal") #here error occurs
re

我的输入文件的片段： 比姆：

1       rs201219564     0       69270   A       G
1       rs2691305       0       69511   A       G
1       rs200505207     0       69761   A       T
1       rs200676709     0       69897   T       C

家庭：

1       1        0 0 1 2
2       2        0 0 1 2
3       3        0 0 1 2

集合ID：

set1_183937        rs1169172101
set1_601436        rs373360530
set1_601667        rs879812396
set1_609407        rs61769279
set1_611317        rs12025928
set1_923421        rs7418179

欧盟

1       69183   rs1333310753    C       T       0       498
1       69200   rs1453226491    T       C       0       496
1       69208   rs1570409667    A       C       0       478
1       69335   rs773188222     G       A       0       1066
1       69404   rs1328728149    T       C       0       1486
1       69428   rs140739101     T       G       20      1652
1       69438   rs758790416     T       C       0       1768
1       69440   rs1424058787    T       G       0       1766
1       69448   rs1366217262    T       A       0       1828
1       69462   rs1217994907    C       G       0       1870

我尝试玩弄 setID 文件，将其更改为：

1:183937        rs1169172101
1:601436        rs373360530
1:601667        rs879812396

但问题依然存在。 我试图在可疑函数中找到问题，但没有发现任何问题：

 > print(rowSums)
    new("standardGeneric",.Data = function (x,na.rm = FALSE,dims = 1,...)
    standardGeneric("rowSums"),generic = "rowSums",package = "base",group = list(),valueClass = character(0),signature = "x",default = new("derivedDefaultMethod",...)
        base::rowSums(x,na.rm = na.rm,dims = dims,...),target = new("signature",.Data = "ANY",names = "x",package = "methods"),defined = new("signature",generic = "rowSums"),skeleton = (new("derivedDefaultMethod",generic = "rowSums"))(x,na.rm,dims,...))
    <bytecode: 0x399c868>
    <environment: 0x39a4718>
    attr(,"generic")
    [1] "rowSums"
    attr(,"generic")attr(,"package")
    [1] "base"
    attr(,"group")
    list()
    attr(,"valueClass")
    character(0)
    attr(,"signature")
    [1] "x"
    attr(,"default")
    Method DeFinition (Class "derivedDefaultMethod"):
    
    function (x,...)
    base::rowSums(x,...)
    <environment: 0x301fa08>
    
    Signatures:
            x
    target  "ANY"
    defined "ANY"
    attr(,"skeleton")
    (new("derivedDefaultMethod",...)
    attr(,"class")
    [1] "standardGeneric"
    attr(,"class")attr(,"package")
    [1] "methods"

先谢谢你！

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