Problems on Import genotype file to R from TASSEL

[wangchunli2024]

Hello Author,
I am now trying to use rMVP package for GWAS analysis. But from the start, I face this problem. May I get some advice and suggestions to solve this problem.

MVP.Data(fileHMP="myG",

•      filePhe="myY",
  

•      sep.hmp="\t",
  

•      sep.phe="\t",
  

•      SNP.effect="Add",
  

•      fileKin=FALSE,
  

•      filePC=FALSE,
  

•      #priority="memory",
  

•      #maxLine=10000,
  

•      out="mvp.hmp"
  

• )
  Preparing data for MVP...
  Error in normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="myG": The system cannot find the file specified
  此外: Warning messages:
  1: In MVP.Data(fileHMP = "myG", filePhe = "myY", sep.hmp = "\t", sep.phe = "\t", :
  SNP.effect has been DEPRECATED.
  2: In MVP.Data(fileHMP = "myG", filePhe = "myY", sep.hmp = "\t", sep.phe = "\t", :
  sep.hmp has been DEPRECATED.

[lariver2]

I am having the same issue. Any help, please?

[wangchunli2024]

we still don't know how to solve this issue and no reply yet from author.

[lariver2]

Do you guys have any real examples using hapmap.txt? My R session is constantly crashing when I use the code you have on your github.
Thank you.

[YinLiLin]

The error pointed out that the system can not find the assigned file, please check if there is a file named 'myG' in your work directory.

[lariver2]

This is the log of the FATAL ERROR in R that TERMINATE the session:
Preparing data for MVP...
Reading file...
Writing map into a file
inds: 163 markers:30520

I tried at least 100 times and kept crashing.

[lariver2]

This is the error when I use the hapmap.txt data as csv file ","
Preparing data for MVP...
Reading file...
Writing map into file
Error: cannot create std::vector larger than max_size()
In addition: Warning messages:
1: In MVP.Data(fileHMP = "hapmap.csv", filePhe = NULL, sep.hmp = ",", :
SNP.effect has been DEPRECATED.
2: In MVP.Data(fileHMP = "hapmap.csv", filePhe = NULL, sep.hmp = ",", :
sep.hmp has been DEPRECATED.

[lariver2]

My hapmap is big:
dim(hapmap)# 30520*174
[1] 30520 174

[YinLiLin]

Hi there! We have updated a new version 1.1.0 on GitHub, in which we have fixed a potential bug of genotype conversion for hapmap file, please feel free to have a try.