GWAS by GAPIT

Question

[md.rabiul27]

I am using GAPIT package in R for GWAS. Already installed the package and import the genotype and phenotype file in R

myY <- read.table("mdp_traits.txt", head = TRUE), myG <- read.table("RabiGeno.hmp.txt", head = FALSE)  and run the GAPIT using command
 myGAPIT <- GAPIT(
Y=myY,
G=myG,
PCA.total=3

And the output is given below:

There is an **Error in plot.window(...) : need finite 'xlim' values** . So, how to solve this problem?

 "--------------------- Welcome to GAPIT ----------------------------"
[1] "Converting genotype..."
[1] "Converting HapMap format to numerical under model of Middle"
[1] "Perform numericalization"
[1] "Succesfuly finished converting HapMap which has bits of 1"
[1] "Converting genotype done."
[1] "Calling prcomp..."
[1] "Creating PCA graphs..."
[1] "Joining taxa..."
[1] "Exporting PCs..."
[1] "PC created"
[1] "Calculating kinship..."
[1] "Number of individuals and SNPs are  182  and  45641"
[1] "Calculating kinship with VanRaden method..."
[1] "substracting P..."
[1] "Getting X'X..."
[1] "Adjusting..."
[1] "Calculating kinship with VanRaden method: done"
[1] "kinship calculated"
[1] "Creating heat map for kinship..."
[1] "Kinship heat map created"
[1] "Adding IDs to kinship..."
[1] "Writing kinship to file..."
[1] "Kinship save as file"
[1] "Kinship created!"
[1] "GAPIT.Genotype.View .Two pdf generate.successfully!"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "GAPIT.Phenotype.View in press..."
[1] "GAPIT.Phenotype.View .output pdf generate.successfully!"
[1] "GAPIT.Phenotype.PCA.View"

**Error in plot.window(...) : need finite 'xlim' values**

In addition: Warning messages:
1: In max(y2[, 2]) : no non-missing arguments to max; returning -Inf
2: In min(y2[, 2]) : no non-missing arguments to min; returning Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
5: In min(x) : no non-missing arguments to min; returning Inf
6: In max(x) :
 Show Traceback

 Rerun with Debug
 Error in plot.window(...) : need finite 'xlim' values

Answer 1

[Philipp Bayer]

I've encountered this before - GAPIT needs numerical values for chromosome names to plot the Manhattan plot. If your chromosomes are named 'Chr1' or so it won't work, they have to be named 1, 2, 3, ....