Error in big.PCA

[TinaNeik]

Hi,

I have 2 questions:

Q1. I meet this problem at the end when running MVP:-

Error in big.PCA(bigMat = big.geno, pcs.to.keep = pcs.keep) :
could not find function "big.PCA"

Here is my script:

> imMVP <- MVP(
+     phe=phenotype,
+     geno=genotype,
+     map=map,
+     #K=Kinship,
+     #CV.GLM=Covariates,
+     #CV.MLM=Covariates,
+     #CV.FarmCPU=Covariates,
+     nPC.GLM=3,
+     nPC.MLM=3,
+     nPC.FarmCPU=3,
+     perc=1,
+     priority="speed",
+     ncpus=12,
+     vc.method="EMMA",
+     maxLoop=10,
+     method.bin="FaST-LMM",#"FaST-LMM","EMMA", "static"
+     #permutation.threshold=TRUE,
+     #permutation.rep=100,
+     threshold=0.05,
+     method=c("GLM", "MLM", "FarmCPU")
+ )
#--------------------------------------------Welcome to MVP---------------------------------------------# 
#          A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For GWAS           # 
# Version: 1.0.1                                                                                        # 
# Authors: Lilin Yin, Haohao Zhang, Zhiwu Zhang, Xinyun Li, Xiaohui Yuan, Shuhong Zhao, and Xiaolei Liu # 
# Contact: xiaoleiliu@mail.hzau.edu.cn                                                                  # 
#-------------------------------------------------------------------------------------------------------# 
[1] "Input data has 34 individuals, 51910 markers"
[1] "Principal Component Analysis Start..."
Error in big.PCA(bigMat = big.geno, pcs.to.keep = pcs.keep) : 
  could not find function "big.PCA"

Q2. I have 38 individuals but it appears that it is reading only 34?

My MVP.Data script looks like this and was successful:

> MVP.Data(fileHMP="~/Desktop/SNP_formatted.hmp.txt",
+          filePhe="~/Desktop/Phenotype.txt",
+          sep.hmp="\t",
+          sep.phe="\t",
+          SNP.effect="Add",
+          fileKin=FALSE,
+          filePC=FALSE,
+          out="mvp.hmp",
+          #priority="memory",
+          #maxLine=10000
+ )
[1] "Preparing data for MVP..."
[1] "Preparation for PHENOTYPE data is done!"
[1] "Output numeric genotype..."
[1] "File: ~/Desktop/myGAPIT/SNP_Rlm7_formatted.hmp.txt ; Total markers:  51910  finished!"
[1] "Preparation for numeric data is done!"
[1] "Output mvp genotype..."
[1] "MVP data prepration accomplished successfully!"

[YinLiLin]

Hi,
Thanks for your using of MVP! Maybe i guess that you installed the version of Unix instead of Windows for MVP, so please make sure the type of your platform, and then chose the right installation way.

[hyacz]

I have edited your comment, please wrap the code with ```, otherwise it is difficult to see clearly.

Q1:
I found that bigpca has removed form CRAN this month. so you should download it from archive

then:

$ R CMD install bigpca_1.1.tar.gz

Q2:
I haven't encountered a similar problem before, maybe you should check your data carefully.

[TinaNeik]

Thank you very much, YinLiLin and hyacz.

Yes, I actually wrongly installed the Windows "devtools" onto the R studio in Mac.

Now I'm trying to install it in Mac but this warning came up:

Warning messages:
1: In install.packages(pkg[p], repos = NULL) :
installation of package ‘snpStats_1.26.0.tar.gz’ had non-zero exit status
2: In install.packages(pkg[p], repos = NULL) :
installation of package ‘MVP_1.0.1.tar.gz’ had non-zero exit status

install.packages(pkg[p], repos = NULL, dependencies=TRUE)
Installing package into ‘/home/tneik/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
ERROR: dependency ‘snpStats’ is not available for package ‘MVP’

Do you have any suggestions how I can solve this please?

Thank you in advance.

[hyacz]

It looks like the Snpsta package fails to install.

You can try the following command in R.

> install.packages('snpStats')

or

> install.packages('<your-path>/snpStats_1.26.0.tar.gz', repos=NULL)

Note: You can find snpStats_1.26.0.tar.gz in the MVP offline installation package

If there are still errors, please send all the logs here.

[TinaNeik]

Thank you very much, hyacz. All good now. I used this:

source("https://bioconductor.org/biocLite.R")
biocLite("snpStats")

[hyacz]

You are welcome. If you have other questions, feel free to open another issue.