yaozhou89 / blink Goto Github PK

Hi Yao,
I got the following error, while I am running BLINK to analysis GWAs.

I used "NA" for myData.dat file as missing values.
thanks :)

setwd("~/Documents/GitHub/BLINK/data")
myGM=read.table("myData.map",head=T)
myGD=read.big.matrix("myData.dat",head=F,sep="\t",type="char")
myY = read.table("myData.txt",head = T)
myBlink=Blink(Y=myY,GD=myGD,GM=myGM,maxLoop=10,time.cal=T)
[1] "----------------------Welcome to Blink----------------------"

Error in cleanupcols(cols, ncol(x), colnames(x)) :

Illegal column index usage in extraction.
Called from: cleanupcols(cols, ncol(x), colnames(x))
Browse[1]>

myBlink=Blink(Y=myY,GD=myGD,GM=myGM,maxLoop=10,time.cal=T)
[1] "----------------------Welcome to Blink----------------------"
[1] "----------------------Iteration: 1 ----------------------"
[1] "seqQTN:"
NULL
Error in seq.default(1, nchr, by = ncycle) : invalid '(to - from)/by'
In addition: There were 50 or more warnings (use warnings() to see the first 50)

warnings()
Warning messages:
1: In diag(iXX) * ve :
Recycling array of length 1 in vector-array arithmetic is deprecated.
Use c() or as.vector() instead.

2: In diag(iXX) * ve :
Recycling array of length 1 in vector-array arithmetic is deprecated.
Use c() or as.vector() instead.

Dear Mr. Zhou,

I was running a GWAS on fitness - related traits of Spirodela polyrhiza using the Blink method via GAPIT. Blink is starting properly but after the 3rd iteration I am receiving the following error message (see below). Do you know the meaning of this error message and how to debug it? Thank you very much for your help!

[1] "----------------------Welcome to Blink----------------------"
[1] "----------------------Iteration: 1 ----------------------"
[1] "seqQTN:"
NULL
[1] "----------------------Iteration: 2 ----------------------"
[1] "LD remove is working...."
[1] "Number SNPs for LD remove:"
[1] 9
[1] "Model selection based on BIC is working...."
[1] "Number of SNPs for BIC selection:"
[1] 7
[1] "seqQTN:"
[1] 166092 220862 153378 510796 298770
[1] "----------------------Iteration: 3 ----------------------"
[1] "LD remove is working...."
[1] "Number SNPs for LD remove:"
[1] 8
[1] "Model selection based on BIC is working...."
[1] "Number of SNPs for BIC selection:"
[1] 8
error in if (seqQTN.save != 0 & seqQTN.save != -1 & !is.null(seqQTN)) seqQTN = union(seqQTN, :
condition has length > 1

Hello, Yao.

I am running BLINK on my data for GWAS analysis. It worked well for the standard procedure, but when I calculated PCs using prcomp, it showed an error of "Error in svd(x, nu = 0, nv = k) : infinite or missing values in 'x'".

I found the error was due to the "NA" representing the missing genotype in *.dat file. I have also tried "Na", "na" or "NaN", but these did not solve the problem. So I would like to ask what is a proper symbol for missing genotype when calculate PC?

Can you please help assist me in the installation of BLINK? I get the follow error weather I try to install BLINK standalone or using GAPIT. I have updated R and all devtool associated packages.

devtools::install_github("YaoZhou89/BLINK")
Downloading GitHub repo YaoZhou89/BLINK@master
✓ checking for file ‘/private/var/folders/bs/hlk80qzx64j_ynwqhtyh1fh5g62f90/T/RtmpafuNqS/remotescf937ba0f7d/YaoZhou89-BLINK-f89a75a/DESCRIPTION’ ...
─ preparing ‘BLINK’:
✓ checking DESCRIPTION meta-information ...
─ excluding invalid files
Subdirectory 'man' contains invalid file names:
‘User Manual.md’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Removed empty directory ‘BLINK/man’
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘BLINK_0.1.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/Users/brice6/Library/R/3.6/library’
(as ‘lib’ is unspecified)

• installing source package ‘BLINK’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** byte-compile and prepare package for lazy loading
  Error: (converted from warning) package ‘foreach’ was built under R version 3.6.2
  Execution halted
  ERROR: lazy loading failed for package ‘BLINK’
• removing ‘/Users/brice6/Library/R/3.6/library/BLINK’
  Error: Failed to install 'BLINK' from GitHub:
  (converted from warning) installation of package ‘/var/folders/bs/hlk80qzx64j_ynwqhtyh1fh5g62f90/T//RtmpafuNqS/filecf93484edb81/BLINK_0.1.0.tar.gz’ had non-zero exit status

I have been using BLINK.R for GWAS. now when I try it after a while, it doesn't send the results in the working directory
would you please help?

i tried to install BLINK for GWAS analysis but it shows following error
Error: Failed to install 'BLINK' from GitHub:
(converted from warning) cannot remove prior installation of package ‘Rcpp’
Actually, it used to download automatically from GAPIT when i selected model "BLINK"

Anybody could help me.