FamRvTest command - Revision history

Shuang Feng: /* Overview of Options */

2014-07-14T05:48:37Z

Overview of Options

Shuang Feng: /* Overview of Options */

2014-07-14T05:47:29Z

Overview of Options

← Older revision		Revision as of 01:47, 14 July 2014
Line 28:		Line 28:

	===Input/Output Options===		===Input/Output Options===
	--ped		--ped: merlin format ped file.
			--dat: merlin format dat file.
			--vcf: vcf file
			--groupFile: gene group file for gene level tests
			--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.
			--prefix: output file prefix
			===VC options===
			--inverseNormal: trait will be inverse normalized before analysis
			--useCovariates: covariates saved in ped file will be adjusted
			--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.

			=== Single Variant Tests===
			--SingleVarScore: the score test
			===Burden Tests===
			--burden: the unweighted burden test
			--MB: the Madsen-Browning weighted burden test
			--VT: the variable threshold test
			--SKAT_BETA: the beta density weighted SKAT test (the original test)
			--SKAT_UW: the unweighted SKAT test
			--SKAT_MB: the Madsen-Browning weighted SKAT test

			===Other Options===
			--freqFile []: allow users to enter frequency of markers from a file
			--annotation: allow users to group variants based on annotation
			--maf: maf cutoff for markers to be grouped for gene-level tests
			--miss: the genotype calling missing rate filter before grouping variants for gene-level tests
			--simulate: allows an integer for number of permutations requested in single variant score test
			--dosage: the flag to tell use dosage saved in VCF file, instead of genotype
			--founderFreq: use founder frequencies for grouping and weighting

Shuang Feng: /* Overview of Options */

2014-07-14T05:38:26Z

Overview of Options

← Older revision		Revision as of 01:38, 14 July 2014
Line 6:		Line 6:

	==Overview of Options==		==Overview of Options==

	~~Data File : (-dname)~~
	~~Pedigree File : (-pname)~~

	Options:		Options:
	Kinship Options : --kinGeno, --~~empMaf [0.05]~~, --~~empMiss~~ [~~0.05~~],		Kinship Options : --kinGeno, --kinPedigree, --kinFile [], --kinSave,
	--~~outputX, --outputKin~~, --~~kinFile~~ [],		--kinMaf [0.05], --kinMiss [0.05]
	--~~kinPrefix~~ []		Input/Output Options : --ped [], --dat [], --vcf [], --noeof,
	Input/Output Options : --vcf [], --groupFile [], --~~freqFile~~ [],		--groupFile [], --longOutput [ON], --prefix []
	--prefix []		VC Options : --inverseNormal, --useCovariates, --traitName []
	VC Options : --inverseNormal, ~~--fitSharedEnv, --fitX,~~		Single Variant Tests : --SingleVarScore
	--useCovariates, --traitName []		Burden Tests : --burden, --MB, --VT, --SKAT_BETA, --SKAT_UW,
	~~SingleVar~~ Tests : ~~--SingleVarLRT,~~ --SingleVarScore,		--SKAT_MB
	~~--SingleVarWald~~		Other Options : --freqFile [], --annotation [], --maf [0.05],
	Burden Tests : --~~SKAT~~, --MB, --~~CMC_binary, --CMC_counts~~		--miss [0.05], --simulate, --dosage, --founderFreq
	~~Variable Threshold Tests : --VTasymptotic~~, --~~VTpermute~~, --~~permuteMin [1000]~~,		PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
	--~~permuteMax [3000000]~~
	Other Options : --~~function~~ [], --~~mafMin~~ [~~0.00~~], --~~mafMax~~ [0.50],
	--~~mac~~ [0.~~00], --noStop, --xLabel [X],~~
	~~--Xstart [2699520~~], --~~Xend [154931044]~~, --dosage,
	--founderFreq, --~~h2Only~~, --~~fullResult~~ [ON]

	~~===Crucial Input Files===~~		=== Kinship Options ===
	'''famRvTest''' takes Merlin format pedigree and data file as input. These two files are crucial for the program to run. Please refer to [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html\|'''Merlin'''] documentation for details.		--kinGeno: kinship matrix is estimated from genotype
	===Kinship Options===		--kinPedigree: kinship matrix is estimated from pedigree structure
	--kinGeno ~~allows you to estimate relationship matrix using genotypes; otherwise,~~ kinship matrix ~~based on pedigree structure will be used.~~		--kinFile: kinship matrix is read from a file
	~~--empMaf and --empMiss specifies the cutoff of minor allele frequency and~~ genotype ~~missing rate to filter SNPs for estimating empirical kinship matrix.~~		--kinMaf: the maf cutoff for markers used to estimate kinship
	--~~outputX allows you to save~~ kinship matrix from ~~chromosome X.~~		--kinMiss: the genotype call rate cutoff for markers included to estimate kinship
	--~~outputKin allows you to save the~~ kinship matrix from ~~autosomal matrix if --outputX is also specified.~~
	--~~kinFile allows you~~ to ~~read~~ kinship ~~matrix from a previously saved file.~~
	--~~kinPrefix specifies~~ the ~~file prefix~~ for kinship ~~matrices saved.~~

	===Input/Output Options===		===Input/Output Options===
	--~~vcf specified the name of input vcf file.~~		--ped
	~~--groupFile should be followed by a the name of the groupfile you want to use for gene-level associations.~~
	~~--freqFile allows users to read allele frequencies from a file instead of estimating based on data.~~
	~~--prefix specifies the name of file prefix for all results saved.~~

	~~===SingleVar Tests===~~
	~~--SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.~~

	~~===Burden Tests===~~
	~~--SKAT --MB --CMC_binary --CMC_counts are SKAT, weighted-burden test (Madsen-Browning weight), collapsing burden test and unweighted burden test based on rare allele count.~~

	~~===VT Tests===~~
	~~--VTasymptotic performs variable threshold test and calculate asymptotic p-value.~~
	~~--VTpermute performs variable threshold test and calculate p-value based on permutation.~~
	~~--permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.~~

	~~===Other Options===~~
	~~--function allows grouping by functional annotation when annotated vcf file is used for gene-level association tests.~~
	~~--mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group.~~
	~~--mac [0.0] specify the minimum rare allele count as one of the filters to rare variants to group.~~
	~~--noStop indicating no stopping rule to be used in VT permutation test.~~
	~~--xLabel [X] specifies labels for chromosome X.~~
	~~--Xstart [2699520] and --Xend [154931044] are start and end position of non-pseudo-autosomal region.~~
	~~--founderFreq considers founder allele frequencies in analysis.~~
	~~--h2Only provides a shortcut of calculating heritability only.~~
	~~--fullResult [on] provides results in long format in gene-level association testing, including results from single markers included in analysis.~~

Shuang Feng: /* Useful Pages */

2013-09-10T18:34:14Z

Useful Pages

← Older revision		Revision as of 14:34, 10 September 2013
Line 2:		Line 2:

	[[FamRvTest\|'''famRvTest''' Home Page]]		[[FamRvTest\|'''famRvTest''' Home Page]]

	[[FamRvTest_tutorial\|'''famRvTest''' Tutorial]]		[[FamRvTest_tutorial\|'''famRvTest''' Tutorial]]

Shuang Feng: /* Useful Pages */

2013-09-10T18:34:06Z

Useful Pages

← Older revision		Revision as of 14:34, 10 September 2013
Line 2:		Line 2:

	[[FamRvTest\|'''famRvTest''' Home Page]]		[[FamRvTest\|'''famRvTest''' Home Page]]
			[[FamRvTest_tutorial\|'''famRvTest''' Tutorial]]

	==Overview of Options==		==Overview of Options==

Shuang Feng: /* Useful Pages */

2013-09-10T18:33:00Z

Useful Pages

← Older revision		Revision as of 14:33, 10 September 2013
Line 1:		Line 1:
	==Useful Pages==		==Useful Pages==

	[[FamRvTest\|'''famRvTest''' Home Page]]		[[FamRvTest\|'''famRvTest''' Home Page]]

	==Overview of Options==		==Overview of Options==

Shuang Feng: /* Overview of Options */

2013-09-10T18:32:45Z

Overview of Options

← Older revision		Revision as of 14:32, 10 September 2013
Line 1:		Line 1:
			==Useful Pages==
			[[FamRvTest\|'''famRvTest''' Home Page]]
	==Overview of Options==		==Overview of Options==

Shuang Feng at 18:31, 10 September 2013

2013-09-10T18:31:49Z

← Older revision		Revision as of 14:31, 10 September 2013
Line 1:		Line 1:
			==Overview of Options==
	Data File : (-dname)
			Data File : (-dname)
	Pedigree File : (-pname)		Pedigree File : (-pname)

Line 21:		Line 22:
	--founderFreq, --h2Only, --fullResult [ON]		--founderFreq, --h2Only, --fullResult [ON]

	Crucial Input Files:		===Crucial Input Files===
	'''famRvTest''' takes Merlin format pedigree and data file as input. These two files are crucial for the program to run. Please refer to [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html\|'''Merlin'''] documentation for details.		'''famRvTest''' takes Merlin format pedigree and data file as input. These two files are crucial for the program to run. Please refer to [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html\|'''Merlin'''] documentation for details.
	Kinship Options:		===Kinship Options===
	--kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used.		--kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used.
	--empMaf and --empMiss specifies the cutoff of minor allele frequency and genotype missing rate to filter SNPs for estimating empirical kinship matrix.		--empMaf and --empMiss specifies the cutoff of minor allele frequency and genotype missing rate to filter SNPs for estimating empirical kinship matrix.
Line 31:		Line 32:
	--kinPrefix specifies the file prefix for kinship matrices saved.		--kinPrefix specifies the file prefix for kinship matrices saved.

	Input/Output Options:		===Input/Output Options===
	--vcf specified the name of input vcf file.		--vcf specified the name of input vcf file.
	--groupFile should be followed by a the name of the groupfile you want to use for gene-level associations.		--groupFile should be followed by a the name of the groupfile you want to use for gene-level associations.
Line 37:		Line 38:
	--prefix specifies the name of file prefix for all results saved.		--prefix specifies the name of file prefix for all results saved.

	SingleVar Tests:		===SingleVar Tests===
	--SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.		--SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.

	Burden Tests:		===Burden Tests===
	--SKAT --MB --CMC_binary --CMC_counts are SKAT, weighted-burden test (Madsen-Browning weight), collapsing burden test and unweighted burden test based on rare allele count.		--SKAT --MB --CMC_binary --CMC_counts are SKAT, weighted-burden test (Madsen-Browning weight), collapsing burden test and unweighted burden test based on rare allele count.

	VT Tests:		===VT Tests===
	--VTasymptotic performs variable threshold test and calculate asymptotic p-value.		--VTasymptotic performs variable threshold test and calculate asymptotic p-value.
	--VTpermute performs variable threshold test and calculate p-value based on permutation.		--VTpermute performs variable threshold test and calculate p-value based on permutation.
	--permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.		--permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.

	Other Options:		===Other Options===
	--function allows grouping by functional annotation when annotated vcf file is used for gene-level association tests.		--function allows grouping by functional annotation when annotated vcf file is used for gene-level association tests.
	--mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group.		--mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group.

Shuang Feng: Created page with " Data File : (-dname) Pedigree File : (-pname) Options: Kinship Options : --kinGeno, --emp..."

2013-09-10T18:18:24Z

Created page with " Data File : (-dname) Pedigree File : (-pname) Options: Kinship Options : --kinGeno, --emp..."

New page

Data File : (-dname)
Pedigree File : (-pname)

Options:
Kinship Options : --kinGeno, --empMaf [0.05], --empMiss [0.05],
--outputX, --outputKin, --kinFile [],
--kinPrefix []
Input/Output Options : --vcf [], --groupFile [], --freqFile [],
--prefix []
VC Options : --inverseNormal, --fitSharedEnv, --fitX,
--useCovariates, --traitName []
SingleVar Tests : --SingleVarLRT, --SingleVarScore,
--SingleVarWald
Burden Tests : --SKAT, --MB, --CMC_binary, --CMC_counts
Variable Threshold Tests : --VTasymptotic, --VTpermute, --permuteMin [1000],
--permuteMax [3000000]
Other Options : --function [], --mafMin [0.00], --mafMax [0.50],
--mac [0.00], --noStop, --xLabel [X],
--Xstart [2699520], --Xend [154931044], --dosage,
--founderFreq, --h2Only, --fullResult [ON]

Crucial Input Files:
'''famRvTest''' takes Merlin format pedigree and data file as input. These two files are crucial for the program to run. Please refer to [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html|'''Merlin'''] documentation for details.
Kinship Options:
--kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used.
--empMaf and --empMiss specifies the cutoff of minor allele frequency and genotype missing rate to filter SNPs for estimating empirical kinship matrix.
--outputX allows you to save kinship matrix from chromosome X.
--outputKin allows you to save the kinship matrix from autosomal matrix if --outputX is also specified.
--kinFile allows you to read kinship matrix from a previously saved file.
--kinPrefix specifies the file prefix for kinship matrices saved.

Input/Output Options:
--vcf specified the name of input vcf file.
--groupFile should be followed by a the name of the groupfile you want to use for gene-level associations.
--freqFile allows users to read allele frequencies from a file instead of estimating based on data.
--prefix specifies the name of file prefix for all results saved.

SingleVar Tests:
--SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.

Burden Tests:
--SKAT --MB --CMC_binary --CMC_counts are SKAT, weighted-burden test (Madsen-Browning weight), collapsing burden test and unweighted burden test based on rare allele count.

VT Tests:
--VTasymptotic performs variable threshold test and calculate asymptotic p-value.
--VTpermute performs variable threshold test and calculate p-value based on permutation.
--permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.

Other Options:
--function allows grouping by functional annotation when annotated vcf file is used for gene-level association tests.
--mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group.
--mac [0.0] specify the minimum rare allele count as one of the filters to rare variants to group.
--noStop indicating no stopping rule to be used in VT permutation test.
--xLabel [X] specifies labels for chromosome X.
--Xstart [2699520] and --Xend [154931044] are start and end position of non-pseudo-autosomal region.
--founderFreq considers founder allele frequencies in analysis.
--h2Only provides a shortcut of calculating heritability only.
--fullResult [on] provides results in long format in gene-level association testing, including results from single markers included in analysis.

← Older revision		Revision as of 01:48, 14 July 2014
Line 20:		Line 20:
	PhoneHome : --noPhoneHome, --phoneHomeThinning [100]		PhoneHome : --noPhoneHome, --phoneHomeThinning [100]

	=== Kinship Options ===		===Kinship Options ===
	--kinGeno: kinship matrix is estimated from genotype		--kinGeno: kinship matrix is estimated from genotype

	--kinPedigree: kinship matrix is estimated from pedigree structure		--kinPedigree: kinship matrix is estimated from pedigree structure

	--kinFile: kinship matrix is read from a file		--kinFile: kinship matrix is read from a file

	--kinMaf: the maf cutoff for markers used to estimate kinship		--kinMaf: the maf cutoff for markers used to estimate kinship

	--kinMiss: the genotype call rate cutoff for markers included to estimate kinship		--kinMiss: the genotype call rate cutoff for markers included to estimate kinship

	===Input/Output Options===		===Input/Output Options===

	--ped: merlin format ped file.		--ped: merlin format ped file.

	--dat: merlin format dat file.		--dat: merlin format dat file.

	--vcf: vcf file		--vcf: vcf file

	--groupFile: gene group file for gene level tests		--groupFile: gene group file for gene level tests

	--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.		--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.

	--prefix: output file prefix		--prefix: output file prefix

	===VC options===		===VC options===

	--inverseNormal: trait will be inverse normalized before analysis		--inverseNormal: trait will be inverse normalized before analysis

	--useCovariates: covariates saved in ped file will be adjusted		--useCovariates: covariates saved in ped file will be adjusted

	--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.		--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.


	=== Single Variant Tests===		=== Single Variant Tests===

	--SingleVarScore: the score test		--SingleVarScore: the score test

	===Burden Tests===		===Burden Tests===

	--burden: the unweighted burden test		--burden: the unweighted burden test

	--MB: the Madsen-Browning weighted burden test		--MB: the Madsen-Browning weighted burden test

	--VT: the variable threshold test		--VT: the variable threshold test

	--SKAT_BETA: the beta density weighted SKAT test (the original test)		--SKAT_BETA: the beta density weighted SKAT test (the original test)

	--SKAT_UW: the unweighted SKAT test		--SKAT_UW: the unweighted SKAT test

	--SKAT_MB: the Madsen-Browning weighted SKAT test		--SKAT_MB: the Madsen-Browning weighted SKAT test


	===Other Options===		===Other Options===

	--freqFile []: allow users to enter frequency of markers from a file		--freqFile []: allow users to enter frequency of markers from a file

	--annotation: allow users to group variants based on annotation		--annotation: allow users to group variants based on annotation

	--maf: maf cutoff for markers to be grouped for gene-level tests		--maf: maf cutoff for markers to be grouped for gene-level tests

	--miss: the genotype calling missing rate filter before grouping variants for gene-level tests		--miss: the genotype calling missing rate filter before grouping variants for gene-level tests

	--simulate: allows an integer for number of permutations requested in single variant score test		--simulate: allows an integer for number of permutations requested in single variant score test

	--dosage: the flag to tell use dosage saved in VCF file, instead of genotype		--dosage: the flag to tell use dosage saved in VCF file, instead of genotype

	--founderFreq: use founder frequencies for grouping and weighting		--founderFreq: use founder frequencies for grouping and weighting