# not working, error: --linear requires scalar phenotype
require(collr)
setwd("/media/data1/kaiyin/RS123_1KG")
argscoll = getPlinkParam(
allow_no_sex = "",
missing_phenotype = 9999,
pheno = "RS123.1kg.pheno/eyecolordata.csv",
covar = "RS123.1kg.pheno/eyecolordata.csv",
covar_name = "sex,age",
linear = "hide-covar",
pheno_name = "ec"
)
taskRoutine(
taskname="eyecolor_ec_s200",
plinkParamList=argscoll,
nMaxShift=200,
initGwas = TRUE,
pvalThresh=1e-3
)
require(collr)
setwd("/media/data1/kaiyin/RS123_1KG")
argscoll = getPlinkParam(
allow_no_sex = "",
missing_phenotype = 9999,
pheno = "RS123.1kg.pheno/eyecolordata.csv",
covar = "RS123.1kg.pheno/eyecolordata.csv",
covar_name = "sex,age",
linear = "hide-covar",
pheno_name = "fan"
)
taskRoutine(
taskname="eyecolor_fan_s200",
plinkParamList=argscoll,
nMaxShift=200,
initGwas = TRUE,
pvalThresh=1e-3
)
require(collr)
setwd("/media/data1/kaiyin/RS123_1KG")
argscoll = getPlinkParam(
allow_no_sex = "",
missing_phenotype = 9999,
pheno = "RS123.1kg.pheno/eyecolordata.csv",
covar = "RS123.1kg.pheno/eyecolordata.csv",
covar_name = "sex,age",
linear = "hide-covar",
pheno_name = "epc2"
)
taskRoutine(
taskname="eyecolor_epc2_s200",
plinkParamList=argscoll,
nMaxShift=200,
initGwas = TRUE,
pvalThresh=1e-3
)
require(collr)
setwd("/media/data1/kaiyin/RS123_1KG")
argscoll = getPlinkParam(
allow_no_sex = "",
missing_phenotype = 9999,
pheno = "RS123.1kg.pheno/eyecolordata.csv",
covar = "RS123.1kg.pheno/eyecolordata.csv",
covar_name = "sex,age",
linear = "hide-covar",
pheno_name = "epc1"
)
taskRoutine(
taskname="eyecolor_epc1_s200",
plinkParamList=argscoll,
nMaxShift=200,
initGwas = TRUE,
pvalThresh=1e-3
)
require(collr)
setwd("/media/data1/kaiyin/RS123_1KG")
argscoll = getPlinkParam(
allow_no_sex = "",
missing_phenotype = 9999,
pheno = "RS123.1kg.pheno/eyecolordata.csv",
covar = "RS123.1kg.pheno/eyecolordata.csv",
covar_name = "sex,age",
linear = "hide-covar",
pheno_name = "s"
)
taskRoutine(
taskname="eyecolor_s_s200",
plinkParamList=argscoll,
nMaxShift=200,
initGwas = TRUE,
pvalThresh=1e-3
)
require(collr)
setwd("/media/data1/kaiyin/RS123_1KG")
argscoll = getPlinkParam(
allow_no_sex = "",
missing_phenotype = 9999,
pheno = "RS123.1kg.pheno/eyecolordata.csv",
covar = "RS123.1kg.pheno/eyecolordata.csv",
covar_name = "sex,age",
linear = "hide-covar",
pheno_name = "h"
)
taskRoutine(
taskname="eyecolor_h_s200",
plinkParamList=argscoll,
nMaxShift=200,
initGwas = TRUE,
pvalThresh=1e-3
)
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