ADJUSTALLELESSIMPLE - winkusch/Easy2 GitHub Wiki

Adjust allele directions according to reference allele directions.

FUNCTION	PARAMETER	DEFAULT	DESCRIPTION
ADJUSTALLELESSIMPLE	--colInA1		Column name of the input Allele1.
ADJUSTALLELESSIMPLE	--colInA2		Column name of the input Allele2
ADJUSTALLELESSIMPLE	--colRefA1		Column name of the reference Allele1.
ADJUSTALLELESSIMPLE	--colRefA2		Column name of the reference Allele2.
ADJUSTALLELESSIMPLE	--acolInFreq		Array of multiple frequency columns that refer to the given alleles. In case the allele direction will be switched in order to match the reference alleles, ALL these columns will be adjusted for the respective SNPs by changing the direction: FreqAdjusted = 1- Freq.
ADJUSTALLELESSIMPLE	--acolInBeta		Array of multiple beta columns that refer to the given alleles. In case the allele direction will be switched in order to match the reference alleles, ALL these columns will be adjusted for the respective SNPs by changing the effect direction: BetaAdjusted = - Beta.
ADJUSTALLELESSIMPLE	--acolInOr		Array of multiple odds ratio columns that refer to the given alleles. In case the allele direction will be switched in order to match the reference alleles, ALL these columns will be adjusted for the respective SNPs by changing the odds ratio as: ORAdjusted = 1/OR.
ADJUSTALLELESSIMPLE	--blnWriteMissingIn	TRUE	Boolean whether variants from input that are missing in Ref should be written to separate file.
ADJUSTALLELESSIMPLE	--blnRemoveMissingIn	FALSE	Boolean whether variants from input that are missing in Ref should be removed.
ADJUSTALLELESSIMPLE	--blnWriteMissingRef	TRUE	Boolean whether variants from reference that are missing in Input should be written to separate file.
ADJUSTALLELESSIMPLE	--blnRemoveMissingRef	FALSE	Boolean whether variants from reference that are missing in Input should be removed.
ADJUSTALLELESSIMPLE	--blnWriteMismatch	TRUE	Boolean value to define whether allele mismatches between the input and reference will be written to a separate file in the output path. Mis-match definition: SNPs that carry valid alleles (defined as ‘A’,’C,’G’,’T’,’I’,’D’) but cannot be matched between input and reference: For example if a SNP is coded A/T in the input, and A/G in the reference file. Optional. Default: 1 Please use [0
ADJUSTALLELESSIMPLE	--blnRemoveMismatch	FALSE	Boolean value to define whether allele mismatches between the input and reference will be removed from the input. Optional. Default: 0. Please use [0
ADJUSTALLELESSIMPLE	--strTag	AAS	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.

Example:

## Allign women alleles to men alleles and change freq/beta accordingly
ADJUSTALLELESSIMPLE --colRefA1 ea.men
--colRefA2 oa.men
--colInA1 ea.women
--colInA2 oa.women
--acolInFreq eaf.women
--acolInBeta beta.women
--strTag AAS.women2men