Error: object 'mysimulation' not found and Error: object 'FALS' not found

[sujee119]

Hi,

I used GAPIT few months ago and it worked perfectly, Now i ran GAPIT functions after getting new data and these errors pops out. I tried using the old data as it is, but same happens. Please Help!

library("GAPIT")
geno <- read.csv("geno_rice.csv", head = FALSE) #local folder (source=http://zzlab.net/GAPIT/data/mdp_traits.txt)
pheno <- read.csv("rca.csv", head = TRUE) #local folder source=http://zzlab.net/GAPIT/data/mdp_genotype_test.hmp.txt)
Gapitdata <- GAPIT(
Y=pheno,
G=geno,
PCA.total=5,
SNP.MAF=0.05,
Multiple_analysis= TRUE,
model=c("GLM","MLM","SUPER","MLMM","FarmCPU","Blink"),
Random.model=FALS
)
[1] "--------------------- Welcome to GAPIT ----------------------------"
[1] "GLM" "MLM" "SUPER" "MLMM" "FarmCPU" "Blink"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "The 1 model in all."
[1] "GLM"
[1] "GAPIT.DP in process..."
[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 2"
[1] "Converting genotype done."
[1] "GAPIT will filter marker with MAF setting !!"
[1] "The markers will be filtered by SNP.MAF: 0.05"
maf_index
FALSE TRUE
12473 21803
[1] "Calculating kinship..."
[1] "Number of individuals and SNPs are 288 and 21803"
[1] "Calculating ZHANG relationship defined by Zhiwu Zhang..."
[1] "substracting mean..."
[1] "Getting X'X..."
[1] "Adjusting..."
[1] "Adjustment by the minimum diagonal"
[1] "Calculating kinship with Zhang 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] "Calling prcomp..."
[1] "Creating PCA graphs..."
[1] "Joining taxa..."
[1] "Exporting PCs..."
[1] "PC created"
[1] "Filting marker for GAPIT.Genotype.View function ..."
[1] "GAPIT.Genotype.View . pdfs generate.successfully!"
[1] 288 6
[1] "GAPIT.DP accomplished successfully for multiple traits. Results are saved"
Error: object 'FALS' not found
In addition: There were 50 or more warnings (use warnings() to see the first 50)

myGAPIT <- GAPIT(
Y=pheno,
G=geno,
model=c("GLM","MLM","SUPER","MLMM","FarmCPU","Blink"),
PCA.total=3,
NJtree.group=4,
QTN.position=mysimulation$QTN.position,
Inter.Plot=TRUE,
Multiple_analysis=TRUE,
PCA.3d=TRUE,
file.output=T
)
[1] "--------------------- Welcome to GAPIT ----------------------------"
[1] "GLM" "MLM" "SUPER" "MLMM" "FarmCPU" "Blink"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "The 1 model in all."
[1] "GLM"
[1] "GAPIT.DP in process..."
[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 2"
[1] "Converting genotype done."
[1] "GAPIT will filter marker with MAF setting !!"
[1] "The markers will be filtered by SNP.MAF: 0"
maf_index
TRUE
34276
[1] "Calculating kinship..."
[1] "Number of individuals and SNPs are 288 and 34276"
[1] "Calculating ZHANG relationship defined by Zhiwu Zhang..."
[1] "substracting mean..."
[1] "Getting X'X..."
[1] "Adjusting..."
[1] "Adjustment by the minimum diagonal"
[1] "Calculating kinship with Zhang method: done"
[1] "kinship calculated"
[1] "Creating heat map for kinship..."
[1] "Kinship heat map created"
[1] "Creating NJ Tree for kinship..."
[1] "Kinship NJ TREE PDF created!"
[1] "Adding IDs to kinship..."
[1] "Writing kinship to file..."
[1] "Kinship save as file"
[1] "Kinship created!"
[1] "Calling prcomp..."
[1] "Creating PCA graphs..."
Loading required package: rgl
This build of rgl does not include OpenGL functions. Use
rglwidget() to display results, e.g. via options(rgl.printRglwidget = TRUE).
Loading required package: rglwidget
The functions in the rglwidget package have been moved to rgl.
Loading required package: htmltools
Loading required package: manipulateWidget
[1] "Joining taxa..."
[1] "Exporting PCs..."
[1] "PC created"
[1] "Filting marker for GAPIT.Genotype.View function ..."
[1] "GAPIT.Genotype.View . pdfs generate.successfully!"
[1] 288 4
[1] "GAPIT.DP accomplished successfully for multiple traits. Results are saved"
Error: object 'mysimulation' not found
In addition: There were 50 or more warnings (use warnings() to see the first 50)

[jiabowang]

Hi,
From your report, I can not find "QTN.position=mysimulation$QTN.position".