For analysis tool developer
GRAB package provides a generic framework of GWAS on a large-scale biobank data. The below gives a brief idea about how to incorporate a new tool into GRAB package.
Suppose that the method is ABCDE, then the following functions are required.
- checkControl.NullModel.ABCDE(control, optionGRM)
- fitNullModel.ABCDE(response, designMat, subjData, control, optionGRM, genoType, markerInfo)
- checkControl.Marker.ABCDE(control, optionGRM)
- checkControl.Region.ABCDE(control, optionGRM)
Function checkControl.NullModel.ABCDE
Input
- control: a list of parameters
- optionGRM:
Output
- control: a list
Function fitNullModel.ABCDE
The function fitNullModel.ABCDE is a lower function to fit null model based on appraoch ABCDE. In main function GRAB.NullModel, the input is first converted to the following data, which is then passed to function fitNullModel.ABCDE.
Input
- response: output of function
model.response - designMat: output of function
model.matrixafter removing column of(Intercept)if any. - subjData: subject ID
- control: output of function
checkControl.NullModel. - optionGRM:
"SparseGRM"or"DenseGRM" - genoType:
"PLINK"or"BGEN" - markerInfo: a data frame to record marker infomation used in GRM construction.
Output
- control: a list