JM: Association mapping or linkage mapping analysis in...
In JunhuiLi1017/JM4QTN: Joint Mapping for QTN

Description Usage Arguments Details Value Author(s) References Examples

Joint Mapping for single trait in multiple-line cross populations based on linear regression

1	JM(vecPheno, vecH2, PhenoData, method, vecThrVal, GenoData_EST, GenoData_QTL)

`vecPheno`	The vector for interest traits name
`vecH2`	Heritability of interest traits respectively
`PhenoData`	The data frame for interest trait, and the first fourth column is fixed
`method`	Method for association mapping(AM) or linkage mapping(LM)
`vecThrVal`	A vector of threshold value
`GenoData_EST`	Information of all marker genotype, where missing markers are estimated
`GenoData_QTL`	Information of all marker genotype with determined distance step, where missing markers are estimated, this dataset is invalid for association mapping(AM)

Some required files must be prepared, including GenoData, PhenoData and others

$traitname

Result of JM for interest trait

Junhui Li

Liu, W., Reif, J. C., Ranc, N., Porta, G. D., and Wurschum, T. (2012). Comparison of biometrical approaches for qtl detection in multiple segregating families. Theoretical and Applied Genetics, 125(5), 987-998.

Steinhoff, J., Liu, W., Maurer, H. P., Wurschum, T., Friedrich, H. L. C., and Ranc, N., et al. (2011). Multiple-line cross quantitative trait locus mapping in european elite maize. Crop Science, 51(6), 2505.

data(GenoData)
data(PhenoData)
data(GenoData_EST)
data(GenoData_S2)
method <- "LM"
vecPheno <- c("newEC1","newEC2")
croType <- "RIL"
GenoData_QTL <- GenoData_S2
#vecThrVal <- c(0.0001,0.0001,0.05,0.05) #for association mapping
vecThrVal <- c(0.0001,0.0001,3.3,3.2)
vecH2 <- c(0.896,0.865)
#QTLresult <- JM(vecPheno, vecH2, PhenoData, method, vecThrVal, GenoData_EST, GenoData_QTL)