Famrvtest - Revision history

Ppwhite: /* PED and DAT Files */

2017-02-21T14:34:41Z

PED and DAT Files

← Older revision		Revision as of 10:34, 21 February 2017
Line 49:		Line 49:
	=== PED and DAT Files ===		=== PED and DAT Files ===
	* When PED file has genotypes saved, there is no need for a VCF file as input.		* When PED file has genotypes saved, there is no need for a VCF file as input.
	* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html '''Merlin'''] format. Please refer to [http://~~csg.~~sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.		* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html '''Merlin'''] format. Please refer to [http://sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
	* An example PED file is in the following:		* An example PED file is in the following:
	1 1 0 0 1 1.5 1 23 A A A A A A A A A A		1 1 0 0 1 1.5 1 23 A A A A A A A A A A

Ppwhite: /* PED and DAT Files */

2017-02-01T17:07:31Z

PED and DAT Files

← Older revision		Revision as of 13:07, 1 February 2017
Line 49:		Line 49:
	=== PED and DAT Files ===		=== PED and DAT Files ===
	* When PED file has genotypes saved, there is no need for a VCF file as input.		* When PED file has genotypes saved, there is no need for a VCF file as input.
	* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html \|'''Merlin'''] format. Please refer to [http://csg.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.		* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html '''Merlin'''] format. Please refer to [http://csg.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
	* An example PED file is in the following:		* An example PED file is in the following:
	1 1 0 0 1 1.5 1 23 A A A A A A A A A A		1 1 0 0 1 1.5 1 23 A A A A A A A A A A

Ppwhite: /* PED and DAT Files */

2017-02-01T17:07:04Z

PED and DAT Files

← Older revision		Revision as of 13:07, 1 February 2017
Line 49:		Line 49:
	=== PED and DAT Files ===		=== PED and DAT Files ===
	* When PED file has genotypes saved, there is no need for a VCF file as input.		* When PED file has genotypes saved, there is no need for a VCF file as input.
	* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html\|'''Merlin'''] format. Please refer to [http://csg.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.		* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html \|'''Merlin'''] format. Please refer to [http://csg.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
	* An example PED file is in the following:		* An example PED file is in the following:
	1 1 0 0 1 1.5 1 23 A A A A A A A A A A		1 1 0 0 1 1.5 1 23 A A A A A A A A A A

Ppwhite: /* PED and DAT Files */

2017-02-01T17:06:25Z

PED and DAT Files

← Older revision		Revision as of 13:06, 1 February 2017
Line 49:		Line 49:
	=== PED and DAT Files ===		=== PED and DAT Files ===
	* When PED file has genotypes saved, there is no need for a VCF file as input.		* When PED file has genotypes saved, there is no need for a VCF file as input.
	* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html\|'''Merlin'''] format. Please refer to [http://~~www~~.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.		* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html\|'''Merlin'''] format. Please refer to [http://csg.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
	* An example PED file is in the following:		* An example PED file is in the following:
	1 1 0 0 1 1.5 1 23 A A A A A A A A A A		1 1 0 0 1 1.5 1 23 A A A A A A A A A A

Shuang Feng: /* Where to Download */

2014-09-29T15:39:20Z

Where to Download

← Older revision		Revision as of 11:39, 29 September 2014
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	* Executable can be downloaded in the following:		* Executable can be downloaded in the following:

	[[Media:Famrvtest.linux.executable.tgz \|Executable for '''LINUX''']]		[[Media:Famrvtest.2.4.linux.executable.tgz \|Executable for '''LINUX''']]

	=== How to Compile ===		=== How to Compile ===

Shuang Feng: /* Group File for Gene-level Tests */

2014-09-28T03:07:50Z

Group File for Gene-level Tests

← Older revision		Revision as of 23:07, 27 September 2014
Line 87:		Line 87:
	PLEKHN1 1:901922:G:A 1:901923:C:A 1:902088:G:A 1:902128:C:T 1:902133:C:G 1:902176:C:T 1:905669:C:G		PLEKHN1 1:901922:G:A 1:901923:C:A 1:902088:G:A 1:902128:C:T 1:902133:C:G 1:902176:C:T 1:905669:C:G
	HES4 1:934735:A:C 1:934770:G:A 1:934801:C:T 1:935085:G:A 1:935089:C:G		HES4 1:934735:A:C 1:934770:G:A 1:934801:C:T 1:935085:G:A 1:935089:C:G
	* Version 2.4 and later allow variants from different chromosomes to be grouped for testing. This might be useful for pathway analysis.		* '''Version 2.4 and later allow variants from different chromosomes to be grouped for testing. This might be useful for pathway analysis.'''
	* '''Note: any variants that have different alleles from listed in group file will be excluded from gene-level tests.'''		* '''Note: any variants that have different alleles from listed in group file will be excluded from gene-level tests.'''

Shuang Feng: /* Group File for Gene-level Tests */

2014-09-28T03:07:35Z

Group File for Gene-level Tests

← Older revision		Revision as of 23:07, 27 September 2014
Line 87:		Line 87:
	PLEKHN1 1:901922:G:A 1:901923:C:A 1:902088:G:A 1:902128:C:T 1:902133:C:G 1:902176:C:T 1:905669:C:G		PLEKHN1 1:901922:G:A 1:901923:C:A 1:902088:G:A 1:902128:C:T 1:902133:C:G 1:902176:C:T 1:905669:C:G
	HES4 1:934735:A:C 1:934770:G:A 1:934801:C:T 1:935085:G:A 1:935089:C:G		HES4 1:934735:A:C 1:934770:G:A 1:934801:C:T 1:935085:G:A 1:935089:C:G
			* Version 2.4 and later allow variants from different chromosomes to be grouped for testing. This might be useful for pathway analysis.
	* '''Note: any variants that have different alleles from listed in group file will be excluded from gene-level tests.'''		* '''Note: any variants that have different alleles from listed in group file will be excluded from gene-level tests.'''

Shuang Feng: /* Group File for Gene-level Tests */

2014-09-28T03:04:12Z

Group File for Gene-level Tests

← Older revision		Revision as of 23:04, 27 September 2014
Line 83:		Line 83:
	GROUP_ID MARKER1_ID MARKER2_ID MARKER3_ID ...		GROUP_ID MARKER1_ID MARKER2_ID MARKER3_ID ...
	* MARKER_ID must be in the following format:		* MARKER_ID must be in the following format:
	CHR:~~POS_ALLELE1/~~ALLELE2		CHR:POS:ALLELE1:ALLELE2
	* An example group file is:		* An example group file is:
	PLEKHN1 1:901922:G:A 1:901923:C:A 1:902088:G:A 1:902128:C:T 1:902133:C:G 1:902176:C:T 1:905669:C:G		PLEKHN1 1:901922:G:A 1:901923:C:A 1:902088:G:A 1:902128:C:T 1:902133:C:G 1:902176:C:T 1:905669:C:G

Shuang Feng: /* Group File for Gene-level Tests */

2014-09-28T03:03:51Z

Group File for Gene-level Tests

← Older revision		Revision as of 23:03, 27 September 2014
Line 85:		Line 85:
	CHR:POS_ALLELE1/ALLELE2		CHR:POS_ALLELE1/ALLELE2
	* An example group file is:		* An example group file is:
	PLEKHN1 1:~~901922_G/~~A 1:~~901923_C/~~A 1:~~902088_G/~~A 1:~~902128_C/~~T 1:~~902133_C/~~G 1:~~902176_C/~~T 1:~~905669_C/~~G		PLEKHN1 1:901922:G:A 1:901923:C:A 1:902088:G:A 1:902128:C:T 1:902133:C:G 1:902176:C:T 1:905669:C:G
	HES4 1:~~934735_A/~~C 1:~~934770_G/~~A 1:~~934801_C/~~T 1:~~935085_G/~~A 1:~~935089_C/~~G		HES4 1:934735:A:C 1:934770:G:A 1:934801:C:T 1:935085:G:A 1:935089:C:G
	* '''Note: any variants that have different alleles from listed in group file will be excluded from gene-level tests.'''		* '''Note: any variants that have different alleles from listed in group file will be excluded from gene-level tests.'''

Shuang Feng: /* Change Log */

2014-09-28T03:02:36Z

Change Log

← Older revision		Revision as of 23:02, 27 September 2014
Line 109:		Line 109:
	* Uploaded new source code package for version2.2, with updated makefiles. (8/4/14)		* Uploaded new source code package for version2.2, with updated makefiles. (8/4/14)
	* Released version 2.3. Fixed a bug which causes compiling error (not finding the correct makefile). (8/20/14)		* Released version 2.3. Fixed a bug which causes compiling error (not finding the correct makefile). (8/20/14)
			* Released version 2.4. Enable analyzing pathways where variants from different chromosomes can be grouped. (9/27/2014)