METAL Quick Start - Revision history

Goncalo: /* Extracting Study by Study Results For Individual SNPs */

2010-04-05T17:11:55Z

Extracting Study by Study Results For Individual SNPs

← Older revision		Revision as of 13:11, 5 April 2010
Line 362:		Line 362:
	The key section of the script is the following one:		The key section of the script is the following one:

			<source lang="text">
	# To restric meta-analysis to two previously reported SNPs		# To restric meta-analysis to two previously reported SNPs
	# and summarize study specific results, uncomment the two		# and summarize study specific results, uncomment the two
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	# ADDFILTER SNP IN (rs10830963,rs563694)		# ADDFILTER SNP IN (rs10830963,rs563694)
	# VERBOSE ON		# VERBOSE ON
			</source>

	To see how the two options work together, first uncomment the last two lines of the script and save the script as "metal-targeted-analysis-script.txt". Next, run METAL:		To see how the two options work together, first uncomment the last two lines of the script and save the script as "metal-targeted-analysis-script.txt". Next, run METAL:

Goncalo: /* Meta-Analysis Results */

2010-04-05T17:11:13Z

Meta-Analysis Results

← Older revision		Revision as of 13:11, 5 April 2010
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	<br>		<br>

	~~ ~~		One good way to understand the contents of this file is to look at the accompanying ''.info'' file. This file describes the contents of each column.

	<source lang="text">		<source lang="text">
Line 324:		Line 324:
	# --> Input File 3 : magic_SARDINIA.tbl		# --> Input File 3 : magic_SARDINIA.tbl
	</source>		</source>

			In this case, a few interesting patterns are worth noting. First, marker rs560887 (near G6PC2) exhibits the strongest evidence for association in the region. Second, you will notice that nearly all markers that make this top ten list have been examined in a total of 6,806 individuals and exhibit consistent directions of effect across studies (these are noted by the pattern of pluses (+) and minuses (-) in the last column). The exception is marker rs853789 which was not examined in the DGI study and thus has a smaller corresponding ''weight'' and a question mark (?) in the first entry of the direction of effect column. When analyzing very large numbers of samples, the direction of effect column allows you to check, at a glance, whether all studies support your strongest findings. If you find that one study consistently suggests an opposite direction of effect for your strongest signals, that might suggest inconsistent labeling of allele 1 and 2 for that study.

	== Refining Your Meta-Analysis ==		== Refining Your Meta-Analysis ==

Goncalo: /* Meta-Analysis Results */

2010-04-05T17:05:46Z

Meta-Analysis Results

← Older revision		Revision as of 13:05, 5 April 2010
Line 244:		Line 244:
	\| -6.597		\| -6.597
	\| 4.189*10<sup>-11</sup>		\| 4.189*10<sup>-11</sup>
	\| <code>~~ ~~?--</code>		\| <code>?--</code>
	\|- align="center"		\|- align="center"
	\| '''rs853773'''		\| '''rs853773'''

Goncalo: /* Meta-Analysis Results */

2010-04-05T17:04:48Z

Meta-Analysis Results

← Older revision		Revision as of 13:04, 5 April 2010
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	\| -7.075		\| -7.075
	\| 1.491*10<sup>-12</sup>		\| 1.491*10<sup>-12</sup>
	\| ---		\| <code>---</code>
	\|- align="center"		\|- align="center"
	\| '''rs853787'''		\| '''rs853787'''
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	\| 6.691		\| 6.691
	\| 2.221*10<sup>-11</sup>		\| 2.221*10<sup>-11</sup>
	\| +++		\| <code>+++</code>
	\|- align="center"		\|- align="center"
	\| '''rs853789'''		\| '''rs853789'''
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	\| -6.597		\| -6.597
	\| 4.189*10<sup>-11</sup>		\| 4.189*10<sup>-11</sup>
	\|  ?--		\| <code> ?--</code>
	\|- align="center"		\|- align="center"
	\| '''rs853773'''		\| '''rs853773'''
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	\| -6.132		\| -6.132
	\| 8.662*10<sup>-10</sup>		\| 8.662*10<sup>-10</sup>
	\| ---		\| <code>---</code>
	\|- align="center"		\|- align="center"
	\| '''rs537183'''		\| '''rs537183'''
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	\| 6.007		\| 6.007
	\| 1.887*10<sup>-9</sup>		\| 1.887*10<sup>-9</sup>
	\| +++		\| <code>+++</code>
	\|- align="center"		\|- align="center"
	\| '''rs557462'''		\| '''rs557462'''
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	\| 6.005		\| 6.005
	\| 1.917*10<sup>-9</sup>		\| 1.917*10<sup>-9</sup>
	\| +++		\| <code>+++</code>
	\|- align="center"		\|- align="center"
	\| '''rs502570'''		\| '''rs502570'''
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	\| -6.001		\| -6.001
	\| 1.955*10<sup>-9</sup>		\| 1.955*10<sup>-9</sup>
	\| ---		\| <code>---</code>
	\|- align="center"		\|- align="center"
	\| '''rs563694'''		\| '''rs563694'''
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	\| 5.975		\| 5.975
	\| 2.300*10<sup>-9</sup>		\| 2.300*10<sup>-9</sup>
	\| +++		\| <code>+++</code>
	\|- align="center"		\|- align="center"
	\| '''rs475612'''		\| '''rs475612'''
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	\| -5.867		\| -5.867
	\| 4.423*10<sup>-9</sup>		\| 4.423*10<sup>-9</sup>
	\| ---		\| <code>---</code>
	\|- align="center"		\|- align="center"
	\| '''rs853781'''		\| '''rs853781'''
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	\| -5.844		\| -5.844
	\| 5.092*10<sup>-9</sup>		\| 5.092*10<sup>-9</sup>
	\| ---		\| <code>---</code>
	\|}		\|}

Goncalo: /* Meta-Analysis Results */

2010-04-05T17:03:10Z

Meta-Analysis Results

← Older revision		Revision as of 13:03, 5 April 2010
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	{\| class="FCK__ShowTableBorders" border="0" cellspacing="1" cellpadding="1" width="80%" align="center"		{\| class="FCK__ShowTableBorders" border="0" cellspacing="1" cellpadding="1" width="80%" align="center"
	\|+ '''Top 10 Meta-Analysis Results'''		\|+ '''Top 10 Meta-Analysis Results'''
	\|-		\|- bgcolor="lightgray"
	! scope="col" \| MarkerName		! scope="col" \| MarkerName
	! scope="col" \| Allele1		! scope="col" \| Allele1
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	! scope="col" \| P-value		! scope="col" \| P-value
	! scope="col" \| Direction		! scope="col" \| Direction
	\|-		\|- align="center"
	\| '''rs560887'''		\| '''rs560887'''
	\| t		\| t
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	\| 1.491*10<sup>-12</sup>		\| 1.491*10<sup>-12</sup>
	\| ---		\| ---
	\|-		\|- align="center"
	\| '''rs853787'''		\| '''rs853787'''
	\| t		\| t
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	\| 2.221*10<sup>-11</sup>		\| 2.221*10<sup>-11</sup>
	\| +++		\| +++
	\|-		\|- align="center"
	\| '''rs853789'''		\| '''rs853789'''
	\| a		\| a
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	\| 4.189*10<sup>-11</sup>		\| 4.189*10<sup>-11</sup>
	\|  ?--		\|  ?--
	\|-		\|- align="center"
	\| '''rs853773'''		\| '''rs853773'''
	\| a		\| a
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	\| 8.662*10<sup>-10</sup>		\| 8.662*10<sup>-10</sup>
	\| ---		\| ---
	\|-		\|- align="center"
	\| '''rs537183'''		\| '''rs537183'''
	\| t		\| t
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	\| 1.887*10<sup>-9</sup>		\| 1.887*10<sup>-9</sup>
	\| +++		\| +++
	\|-		\|- align="center"
	\| '''rs557462'''		\| '''rs557462'''
	\| t		\| t
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	\| 1.917*10<sup>-9</sup>		\| 1.917*10<sup>-9</sup>
	\| +++		\| +++
	\|-		\|- align="center"
	\| '''rs502570'''		\| '''rs502570'''
	\| a		\| a
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	\| 1.955*10<sup>-9</sup>		\| 1.955*10<sup>-9</sup>
	\| ---		\| ---
	\|-		\|- align="center"
	\| '''rs563694'''		\| '''rs563694'''
	\| a		\| a
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	\| 2.300*10<sup>-9</sup>		\| 2.300*10<sup>-9</sup>
	\| +++		\| +++
	\|-		\|- align="center"
	\| '''rs475612'''		\| '''rs475612'''
	\| t		\| t
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	\| 4.423*10<sup>-9</sup>		\| 4.423*10<sup>-9</sup>
	\| ---		\| ---
	\|-		\|- align="center"
	\| '''rs853781'''		\| '''rs853781'''
	\| a		\| a

Goncalo at 17:01, 5 April 2010

2010-04-05T17:01:13Z

← Older revision		Revision as of 13:01, 5 April 2010
Line 211:		Line 211:
	Meta-analysis results are stored in the file 'METAANALYSIS1.TBL'. By default, this file isn't sorted, but you should be able to sort it in a variety of ways. Here are the top 10 smallest p-values as obtained with the UNIX sort command:		Meta-analysis results are stored in the file 'METAANALYSIS1.TBL'. By default, this file isn't sorted, but you should be able to sort it in a variety of ways. Here are the top 10 smallest p-values as obtained with the UNIX sort command:

	{\| class="FCK__ShowTableBorders" border="0" cellspacing="1~~" summary="Table obtained with UNIX command <code>sort -g -k 6 METAANALYSIS1.TBL \| head -10</code>~~" cellpadding="1" width="80%" align="center"		{\| class="FCK__ShowTableBorders" border="0" cellspacing="1" cellpadding="1" width="80%" align="center"
	\|+ Top 10 Meta-Analysis Results		\|+ '''Top 10 Meta-Analysis Results'''
	\|-		\|-
	! scope="col" \| MarkerName		! scope="col" \| MarkerName
	! scope="col" \| Allele1		! scope="col" \| Allele1
	! scope="col" \| Allele2		! scope="col" \| Allele2
	! scope="col" \| Weight		! scope="col" \| Weight
	! scope="col" \| Zscore		! scope="col" \| Zscore
	! scope="col" \| P-value		! scope="col" \| P-value
	! scope="col" \| Direction		! scope="col" \| Direction
	\|-		\|-
	\| '''rs560887'''		\| '''rs560887'''
	\| t		\| t
	\| c		\| c
	\| 6806		\| 6806
	\| -7.075		\| -7.075
	\| 1.491*10<sup>-12</sup>		\| 1.491*10<sup>-12</sup>
	\| ---		\| ---
	\|-		\|-
	\| '''rs853787'''		\| '''rs853787'''
	\| t		\| t
	\| g		\| g
	\| 6806		\| 6806
	\| 6.691		\| 6.691
	\| 2.221*10<sup>-11</sup>		\| 2.221*10<sup>-11</sup>
	\| +++		\| +++
	\|-		\|-
	\| '''rs853789'''		\| '''rs853789'''
	\| a		\| a
	\| g		\| g
	\| 5339		\| 5339
	\| -6.597		\| -6.597
	\| 4.189*10<sup>-11</sup>		\| 4.189*10<sup>-11</sup>
	\| ?--		\|  ?--
	\|-		\|-
	\| '''rs853773'''		\| '''rs853773'''
	\| a		\| a
	\| g		\| g
	\| 6806		\| 6806
	\| -6.132		\| -6.132
	\| 8.662*10<sup>-10</sup>		\| 8.662*10<sup>-10</sup>
	\| ---		\| ---
	\|-		\|-
	\| '''rs537183'''		\| '''rs537183'''
	\| t		\| t
	\| c		\| c
	\| 6806		\| 6806
	\| 6.007		\| 6.007
	\| 1.887*10<sup>-9</sup>		\| 1.887*10<sup>-9</sup>
	\| +++		\| +++
	\|-		\|-
	\| '''rs557462'''		\| '''rs557462'''
	\| t		\| t
	\| c		\| c
	\| 6806		\| 6806
	\| 6.005		\| 6.005
	\| 1.917*10<sup>-9</sup>		\| 1.917*10<sup>-9</sup>
	\| +++		\| +++
	\|-		\|-
	\| '''rs502570'''		\| '''rs502570'''
	\| a		\| a
	\| g		\| g
	\| 6806		\| 6806
	\| -6.001		\| -6.001
	\| 1.955*10<sup>-9</sup>		\| 1.955*10<sup>-9</sup>
	\| ---		\| ---
	\|-		\|-
	\| '''rs563694'''		\| '''rs563694'''
	\| a		\| a
	\| c		\| c
	\| 6806		\| 6806
	\| 5.975		\| 5.975
	\| 2.300*10<sup>-9</sup>		\| 2.300*10<sup>-9</sup>
	\| +++		\| +++
	\|-		\|-
	\| '''rs475612'''		\| '''rs475612'''
	\| t		\| t
	\| c		\| c
	\| 6806		\| 6806
	\| -5.867		\| -5.867
	\| 4.423*10<sup>-9</sup>		\| 4.423*10<sup>-9</sup>
	\| ---		\| ---
	\|-		\|-
	\| '''rs853781'''		\| '''rs853781'''
	\| a		\| a
	\| g		\| g
	\| 6806		\| 6806
	\| -5.844		\| -5.844
	\| 5.092*10<sup>-9</sup>		\| 5.092*10<sup>-9</sup>
	\| ---		\| ---
	\|}		\|}
Line 305:		Line 305:
	<br>		<br>



	<source lang="text">		<source lang="text">

Goncalo: /* Meta-Analysis Results */

2010-04-05T17:00:21Z

Meta-Analysis Results

@@ Line 207: / Line 207: @@
 Note that results are stored in files labeled 'METAANALYSIS1.TBL' and 'METAANALYSIS1.TBL.info'. If you load data for additional studies and repeat the meta-analysis command, those results will be stored in a file named 'METAANALYSIS'''2'''.TBL' and 'METAANALYSIS'''2'''.TBL.info'. You can change default output file names with the <code>OUTFILE</code> command.
-=== Meta-Analysis Results ===
+=== Meta-Analysis Results  ===
 == Refining Your Meta-Analysis ==

Goncalo: /* Describing the SardiNIA Input Files */

2010-04-05T16:46:42Z

Describing the SardiNIA Input Files

← Older revision		Revision as of 12:46, 5 April 2010
Line 169:		Line 169:
	This is the expected output from the above series of commands:		This is the expected output from the above series of commands:

			<source lang="text">
	## Set marker header to SNP ...		## Set marker header to SNP ...
	## Set default weight to 4106.00 ...		## Set default weight to 4106.00 ...
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	## WARNING: No 'N' column found -- using DEFAULTWEIGHT = 4106		## WARNING: No 'N' column found -- using DEFAULTWEIGHT = 4106
	## Processed 2361 markers ...		## Processed 2361 markers ...
			</source>

	=== Executing the Meta-Analysis ===		=== Executing the Meta-Analysis ===

Goncalo: /* Describing the SardiNIA Input Files */

2010-04-05T16:46:19Z

Describing the SardiNIA Input Files

← Older revision		Revision as of 12:46, 5 April 2010
Line 163:		Line 163:

	PROCESS magic_SARDINIA.tbl		PROCESS magic_SARDINIA.tbl
	</~~code~~>		</source>

	In contrast to the previous files, the unique thing about the Sardinia input files is that they include no column detailing the number of individuals analyzed for each marker. Instead, using [Genotype Imputation] all missing genotypes were filled in and exactly 4,106 individuals were analyzed in each row. This is specified with the <code>DEFAULT 4106</code> command.		In contrast to the previous files, the unique thing about the Sardinia input files is that they include no column detailing the number of individuals analyzed for each marker. Instead, using [Genotype Imputation] all missing genotypes were filled in and exactly 4,106 individuals were analyzed in each row. This is specified with the <code>DEFAULT 4106</code> command.

Goncalo: /* Describing the SardiNIA Input Files */

2010-04-05T16:46:03Z

Describing the SardiNIA Input Files

@@ Line 166: / Line 166: @@
 In contrast to the previous files, the unique thing about the Sardinia input files is that they include no column detailing the number of individuals analyzed for each marker. Instead, using [Genotype Imputation] all missing genotypes were filled in and exactly 4,106 individuals were analyzed in each row. This is specified with the <code>DEFAULT 4106</code> command.
 === Executing the Meta-Analysis ===
@@ Line 176: / Line 191: @@
 If you are interested in the possibility of between study heterogeneity, use the <code>ANALYZE HETEROGENEITY</code> command instead.
 === Meta-Analysis Results ===