question re the covariate file

[MNiarchou]

Hi @wzhy2000 ,

I have a question re the covariates file. I would like to integrate in the GWAS variables such as sex, and principal components of ancestry where each subject has one measure, but also two covariates, such as age at the time of weight where each subject has repeated measures. Can you please let me know if this is feasible and also how to format the covariate file accordingly?

Thank you!
Maria

[Yuan199501]

Hello!
I would like to ask you some questions about whether you have encountered such errors after running fGWAS

No curve or new curve type is specified, curve fitting is being performed.
Searching curve type ......

• [ 1 / 10 ] try curve: Logistic
  Error in class(h0) == "try-error" || is.na(h0) :
  'length = 5' in coercion to 'logical(1)'

When I read the phenotypic data

obj.phe2 <- fg.load.phenotype(

• file.phe.long = "D:/soft_study/fGWAS/22YL_565/PDY.csv",
  

• file.phe.cov = "D:/soft_study/fGWAS/22YL_565/phe.cov.csv",
  

• file.phe.time = "D:/soft_study/fGWAS/22YL_565/PDT.csv",
  

• curve.type=NULL,  
  

• covariance.type=NULL,  
  

• file.plot.pdf = "curve.fitting.pdf",
  

• options = list(verbose = TRUE)
  

• )
  [ Loading Phenotype Data]
  Checking the parameters ......

• Phenotypic Data File = D:/soft_study/fGWAS/22YL_565/PDY.csv
• Covariate Data File = D:/soft_study/fGWAS/22YL_565/phe.cov.csv
• Time Data File = D:/soft_study/fGWAS/22YL_565/PDT.csv
• Curve Type = Legendre2
• Covariance Type = AR1
• Intercept = TRUE
  Checking phenotype file......
• PHE.LONG = D:/soft_study/fGWAS/22YL_565/PDY.csv
• Individuals = 565
• Times = 5
• Mean = 885.3225 944.9758 977.31 1028.423 1148.789
• SD = 58.30879 59.47311 59.77077 69.61948 59.33307
  First 5 Items:
  Y_1 Y_2 Y_3 Y_4 Y_5
  Ta000001 891.17 929.17 976.33 1008.68 1135.98
  Ta000003 858.96 949.59 976.33 1000.78 1119.73
  Ta000011 891.17 964.93 989.43 1039.27 1174.47
  Ta000021 909.35 964.93 989.43 1051.28 1174.47
  Ta000033 891.17 949.59 976.33 1017.48 1155.21
• PHE.TIME = D:/soft_study/fGWAS/22YL_565/PDT.csv
• Individuals = 565
• Times = 5
• Mean = 1 2 3 4 5
• SD = 0 0 0 0 0
  First 5 Items:
  Z_1 Z_2 Z_3 Z_4 Z_5
  Ta000001 1 2 3 4 5
  Ta000003 1 2 3 4 5
  Ta000011 1 2 3 4 5
  Ta000021 1 2 3 4 5
  Ta000033 1 2 3 4 5
  Checking covariate file......
• COV.FILE = D:/soft_study/fGWAS/22YL_565/phe.cov.csv
• Individuals = 565
• Covariates = 2
• Mean = 9.090572e-05 3.906469e-06
• SD = 0.0421075 0.0421076
  First 5 Items:
  X_1 X_2
  Ta000001 -0.0261141 0.01996870
  Ta000003 -0.0378563 0.01457520
  Ta000011 -0.0351182 0.01703760
  Ta000021 -0.0363623 -0.00218863
  Ta000033 -0.0413945 -0.06236650
  No curve or new curve type is specified, curve fitting is being performed.
  Searching curve type ......
• [ 1 / 1 ] try curve: Legendre2
  Error in class(h0) == "try-error" || is.na(h0) :
  'length = 5' in coercion to 'logical(1)'