GC - winkusch/Easy2 GitHub Wiki

Genomic control correction. The GC Lambda can be calculated from all SNPs or from a subset of SNPs (see –fileGcSnps); will be written to the report; and can optionally be applied to the data set (see --blnSuppressCorrection).

FUNCTION	PARAMETER	DEFAULT	DESCRIPTION
GC	--colPval		Define P-Value column that will be used for calculating the GC lambda and for the correction.
GC	--colSE		If defined, this Standard error column will be corrected as well.
GC	--numLambda	-1	If defined, this lambda will be used for performing the correction. Optional. Default: NA (causes EasyStrata to calculate the lambda from the specified colPval)
GC	--numChiSqDf	1
GC	--fileGcSnps		If defined, only SNPs from this file will be used for calculating the lambda. Optional. Default: NA (causes EasyStrata to calculate the lambda from the full list of input SNPs)
GC	--colGcSnpsMarker		If fileGcSnps is defined, please define here the Marker column name of the file. Optional. Default: NA (only required if fileGcSnps is specified)
GC	--colInMarker		Column name of the input marker column.
GC	--blnSuppressCorrection	FALSE	"Boolean value. If set to 1 (TRUE), the GC lambda will be calculated, but the actual correction will not be performed. If set to 0 (FALSE), the GC lambda will be calculated and the colPval and colSE (if specified) will be corrected. New columns with the suffix "".GC"" will be added to the GWA data set. Optional. Default: 0; Please use: [0
GC	--strTag	GC	Tag for the function step that will be added to related variables in the REPORT and to related output to ensure unique and easily recognizable file names and REPORT variable names.
GC	--rcdGcCrit