Question: GWAS by GAPIT

1

md.rabiul27 •

**10**wrote: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
```

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modified 12 months ago
by
Biostar ♦♦

**20**• written 18 months ago by md.rabiul27 •**10**