RAREFY TUTORIAL - Revision history

Shuang Feng: /* Useful Wiki Pages */

2015-02-17T09:10:15Z

Useful Wiki Pages

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	* The [[RAREFY \| '''RAREFY Homepage''']]		* The [[RAREFY \| '''RAREFY Homepage''']]
	* The [[RAREFY_DOC \| '''RAREFY Documentation''']]		* The [[RAREFY_DOC \| '''RAREFY Documentation''']]
	* The [[RAREFY_COMMAND \| '''RAREFY ~~COMMAND REFERENCE~~''']]		* The [[RAREFY_COMMAND \| '''RAREFY Command Reference''']]
			* The [[RAREFY_DOWNLOAD \| '''RAREFY Download''']]
	* The [[RAREFY_FAQ \| '''FAQ''']]		* The [[RAREFY_FAQ \| '''FAQ''']]

2015-02-17T08:33:01Z

OUTPUT

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	==OUTPUT==		==OUTPUT==
	*Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in "sim1_simul_rarefy.trait.Decreasing.result" and "sim1_simul_rarefy.trait.~~Decreasing~~.result" separately.		*Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in "sim1_simul_rarefy.trait.Decreasing.result" and "sim1_simul_rarefy.trait.Increasing.result" separately.
			*Use the following command to sort the RAREFY score to select informative individuals:
			sort -k7 -gr sim1_simul_rarefy.trait.Increasing.result \| head -10
			*The top 10 selected individuals are:
			famid pid fatid motid sex residual rarefy_idv_score rarefy_fam_score
			1994 5 1 2 1 4.05563 0.839037 2.73226
			1994 2 0 0 2 3.66226 0.829384 2.73226
			345 1 0 0 1 3.45514 0.785963 1.95526
			345 4 1 2 2 3.20513 0.782924 1.95526
			3503 4 1 2 2 3.33598 0.621358 1.85789
			3503 1 0 0 1 2.15643 0.619741 1.85789
			1994 3 1 2 1 2.25633 0.607197 2.73226
			3503 5 1 2 1 2.51068 0.601241 1.85789
			1994 4 1 2 2 1.85392 0.437127 2.73226
			3860 2 0 0 2 2.45598 0.405228 1.5474

2015-02-17T08:29:08Z

OUTPUT

← Older revision		Revision as of 04:29, 17 February 2015
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	==OUTPUT==		==OUTPUT==
			*Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in "sim1_simul_rarefy.trait.Decreasing.result" and "sim1_simul_rarefy.trait.Decreasing.result" separately.

2015-02-17T08:27:39Z

COMMAND

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	==COMMAND==		==COMMAND==
			*Use the following command to RAREFY the sample for both trait-increasing and trait-decreasing variants. Although this sample includes only trait-increasing variant, in real world, we do not know if the sample contains trait-increasing variants or trait-decreasing variants or both.
			rarefy --ped sim1.ped --dat sim1.dat --inverseNormal --traitIncreasing --traitDecreasing --prefix sim1

	==OUTPUT==		==OUTPUT==

2015-02-17T08:25:26Z

EXAMPLE DATA SET

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	*Please download the [[Media:Rarefy.example.tar.gz \| '''EXAMPLE''']] file to your directory.		*Please download the [[Media:Rarefy.example.tar.gz \| '''EXAMPLE''']] file to your directory.
	*In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.		*In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.
			*A variant with frequency 0.001 and effect size 2 SD was simulated in the sample. The variant was simulated to be trait-increasing.

	==COMMAND==		==COMMAND==

	==OUTPUT==		==OUTPUT==

2015-02-17T08:24:45Z

EXAMPLE DATA SET

← Older revision		Revision as of 04:24, 17 February 2015
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	==EXAMPLE DATA SET==		==EXAMPLE DATA SET==
	*Please download the [[Media:Rarefy.example.tar.gz \| '''EXAMPLE''']] file to your directory.		*Please download the [[Media:Rarefy.example.tar.gz \| '''EXAMPLE''']] file to your directory.
			*In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.

	==COMMAND==		==COMMAND==

	==OUTPUT==		==OUTPUT==

2015-02-17T08:23:02Z

EXAMPLE DATA SET

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	==EXAMPLE DATA SET==		==EXAMPLE DATA SET==
	*Please download the [[~~File~~:Rarefy.example.tar.gz \| '''EXAMPLE''']] file to your directory.		*Please download the [[Media:Rarefy.example.tar.gz \| '''EXAMPLE''']] file to your directory.

	==COMMAND==		==COMMAND==

	==OUTPUT==		==OUTPUT==

2015-02-17T08:22:52Z

EXAMPLE DATA SET

← Older revision		Revision as of 04:22, 17 February 2015
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	==EXAMPLE DATA SET==		==EXAMPLE DATA SET==
	*Please download the [[~~rarefy~~.example.tar.gz \| '''EXAMPLE''']] file to your directory.		*Please download the [[File:Rarefy.example.tar.gz \| '''EXAMPLE''']] file to your directory.

	==COMMAND==		==COMMAND==

	==OUTPUT==		==OUTPUT==

2015-02-17T08:22:33Z

EXAMPLE DATA SET

← Older revision		Revision as of 04:22, 17 February 2015
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	==EXAMPLE DATA SET==		==EXAMPLE DATA SET==
	*Please download the ~~PED and DAT~~ file to your ~~computer~~.		*Please download the [[rarefy.example.tar.gz \| '''EXAMPLE''']] file to your directory.

	==COMMAND==		==COMMAND==

	==OUTPUT==		==OUTPUT==

2015-02-17T07:47:35Z

EXAMPLE DATA SET

← Older revision		Revision as of 03:47, 17 February 2015
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	==EXAMPLE DATA SET==		==EXAMPLE DATA SET==
	*To to ~~uploaded~~.		*Please download the PED and DAT file to your computer.

	==COMMAND==		==COMMAND==

	==OUTPUT==		==OUTPUT==

← Older revision		Revision as of 05:10, 17 February 2015
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	* The [[RAREFY \| '''RAREFY Homepage''']]		* The [[RAREFY \| '''RAREFY Homepage''']]
	* The [[RAREFY_DOC \| '''RAREFY Documentation''']]		* The [[RAREFY_DOC \| '''RAREFY Documentation''']]
	* The [[RAREFY_COMMAND \| '''RAREFY ~~COMMAND REFERENCE~~''']]		* The [[RAREFY_COMMAND \| '''RAREFY Command Reference''']]
			* The [[RAREFY_DOWNLOAD \| '''RAREFY Download''']]
	* The [[RAREFY_FAQ \| '''FAQ''']]		* The [[RAREFY_FAQ \| '''FAQ''']]