MERGE - winkusch/Easy2 GitHub Wiki

Merge reference data (e.g. annotation data like chromosome and position) to each of the input data-sets.

FUNCTION	PARAMETER	DEFAULT	DESCRIPTION
MERGE	--colInMarker		Column name of the input marker column.
MERGE	--strInSuffix		suffix for input table
MERGE	--blnInAll	TRUE	Boolean value to define left inner/outer join. If set to 1 (TRUE), all SNPs from the input will be present in the merged data-set. If set to 0 (FALSE), only SNPs from the input will be present in the merged data-set that are also present in the reference.Optional. Default: 1. Please use: [0
MERGE	--fileRef		Path to the reference data set that will be added.
MERGE	--colRefMarker		SNP column name of the reference. Will be used for merging.
MERGE	--strRefSuffix		suffix for reference table
MERGE	--blnRefAll	FALSE	Boolean value to define right inner/outer join. If set to 1 (TRUE), all SNPs from the reference will be present in the merged data-set. If set to 0 (FALSE), only SNPs from the reference will be present in the merged data-set that are also present in the input.Optional. Default: 0. Please use: [0
MERGE	--fileRefTag	1
MERGE	--blnWriteNotInRef	FALSE	Boolean value to define whether SNPs from the input that are missed in the reference will be written to a separate file in the output path. Optional. Default: 0. Please use: [0
MERGE	--blnWriteNotInIn	FALSE	Boolean value to define whether SNPs from the reference that are missed in the input will be written to a separate file in the output path. Optional. Default: 0. Please use: [0
MERGE	--strTag		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.
MERGE	--strMissing	INHERITED	missing character
MERGE	--strSeparator	INHERITED	column separator string
MERGE	--acolIn	INHERITED	array of columns to read
MERGE	--acolInClasses	INHERITED	array of column types (eg 'character', 'numeric', 'integer' or 'logical')
MERGE	--acolNewName	INHERITED	array of new column names
MERGE	--blnUseFastRead	INHERITED	logical whether fread should be used
MERGE	--numRowSkip	INHERITED
MERGE	--blnCreateCpaid	FALSE
MERGE	--colRefChr		column name of reference chromosome
MERGE	--colRefPos		Column name of the reference position
MERGE	--colRefA1		Column name of the reference Allele1.
MERGE	--colRefA2		Column name of the reference Allele2.
MERGE	--blnSort2Ref	FALSE

Example: MERGE --colInMarker MarkerName
--fileRef /test/referencefile.txt
--strMissing NA --strSep SPACE
--colRefMarker rsID
--strInSuffix .in
--strRefSuffix .ref
--blnInAll 1
--blnRefAll 0
--blnWriteNotInRef 0
--blnWriteNotInIn 0
--strTag REF